Moved most testdata from public to private

public/testdata/Beagle/inttestbgl.gprobs

@@ -1,80 +0,0 @@
-marker alleleA alleleB NA07056 NA07056 NA07056 NA11892 NA11892 NA11892 NA11893 NA11893 NA11893 NA12347 NA12347 NA12347 NA12348 NA12348 NA12348 NA12383 NA12383 NA12383 NA12413 NA12413 NA12413 NA12546 NA12546 NA12546 NA12775 NA12775 NA12775 NA12777 NA12777 NA12777 NA12778 NA12778 NA12778 NA20502 NA20502 NA20502 NA20505 NA20505 NA20505 NA20508 NA20508 NA20508 NA20509 NA20509 NA20509 NA20510 NA20510 NA20510 NA20512 NA20512 NA20512 NA20515 NA20515 NA20515 NA20516 NA20516 NA20516 NA20517 NA20517 NA20517 NA20518 NA20518 NA20518 NA20519 NA20519 NA20519 NA20520 NA20520 NA20520 NA20522 NA20522 NA20522 NA20524 NA20524 NA20524 NA20525 NA20525 NA20525 NA20527 NA20527 NA20527 NA20528 NA20528 NA20528 NA20529 NA20529 NA20529 NA20530 NA20530 NA20530 NA20531 NA20531 NA20531 NA20534 NA20534 NA20534 NA20535 NA20535 NA20535 NA20538 NA20538 NA20538 NA20539 NA20539 NA20539 NA20540 NA20540 NA20540 NA20541 NA20541 NA20541 NA20542 NA20542 NA20542 NA20543 NA20543 NA20543 NA20544 NA20544 NA20544 NA20582 NA20582 NA20582 NA20586 NA20586 NA20586 NA20588 NA20588 NA20588 NA20589 NA20589 NA20589 NA20752 NA20752 NA20752 NA20753 NA20753 NA20753 NA20754 NA20754 NA20754 NA20755 NA20755 NA20755 NA20756 NA20756 NA20756
-20:60251 T C 0.9965 0.0035 0 0.99303 0.00697 0 0.99303 0.00697 0 0.99828 0.00172 0 0.99912 0.00088 0 0.9965 0.0035 0 0.99658 0.00342 0 0.99994 0.00006 0 0 1 0 0.99997 0.00003 0 0.9965 0.0035 0 0.99828 0.00172 0 0.98619 0.01381 0 0.99303 0.00697 0 0.99828 0.00172 0 0.97264 0.02717 0.00019 0.99303 0.00697 0 0.99303 0.00697 0 0.99303 0.00697 0 0.99956 0.00044 0 0.99828 0.00172 0 0.99303 0.00697 0 0.99828 0.00172 0 0.97264 0.02717 0.00019 0.9965 0.0035 0 0.99824 0.00176 0 0.99957 0.00043 0 0.99303 0.00697 0 0.99989 0.00011 0 0.99957 0.00043 0 0.99303 0.00697 0 0.9965 0.0035 0 0.99824 0.00176 0 0.99303 0.00697 0 0.99957 0.00043 0 0.9965 0.0035 0 0.98619 0.01381 0 0.99303 0.00697 0 0.99303 0.00697 0 0.99956 0.00044 0 0.99914 0.00086 0 0.97264 0.02717 0.00019 0.97264 0.02717 0.00019 0.99303 0.00697 0 0.9965 0.0035 0 0.9965 0.0035 0 0.99828 0.00172 0 0.99978 0.00022 0 0.99957 0.00043 0
-20:60864 G C 0.9992 0.0008 0 0.9992 0.0008 0 0.99841 0.00159 0 0.99676 0.00324 0 0.9996 0.0004 0 0.99676 0.00324 0 0.99355 0.00645 0 0.99979 0.00021 0 0.99841 0.00159 0 0.99997 0.00003 0 0.99683 0.00317 0 0.98722 0.01278 0 0.97466 0.02517 0.00017 0.9992 0.0008 0 0.99355 0.00645 0 0.98722 0.01278 0 0.99841 0.00159 0 0.99918 0.00082 0 0.98722 0.01278 0 0.99355 0.00645 0 0.9992 0.0008 0 0.99995 0.00005 0 0.9999 0.0001 0 0.99355 0.00645 0 0.99355 0.00645 0 0.99959 0.00041 0 0.99676 0.00324 0 0.99959 0.00041 0 0 1 0 0.99841 0.00159 0 0.9998 0.0002 0 0.99676 0.00324 0 0.99683 0.00317 0 0.97466 0.02517 0.00017 0.9999 0.0001 0 0.99676 0.00324 0 0.98722 0.01278 0 0.9937 0.0063 0 0.9992 0.0008 0 0.98721 0.01279 0 0.98721 0.01279 0 0.99676 0.00324 0 0.9992 0.0008 0 0.99676 0.00324 0 0.99355 0.00645 0 0.99841 0.00159 0 0.99837 0.00163 0 0.9992 0.0008 0 0.9992 0.0008 0
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-20:63559 C A 0.99477 0.00523 0 0.97955 0.02045 0 0 0.96018 0.03982 0.98987 0.01013 0 0.98967 0.01033 0 0.99786 0.00214 0 0.99872 0.00128 0 0.97955 0.02045 0 0.99481 0.00519 0 1 0 0 0.98972 0.01028 0 0.98986 0.01014 0 0.99118 0.00882 0 0.99479 0.00521 0 0.99867 0.00133 0 0.98966 0.01034 0 0.99748 0.00252 0 0.99967 0.00033 0 0.98996 0.01004 0 0.97953 0.02047 0 0.99999 0.00001 0 0.99967 0.00033 0 1 0 0 0.99869 0.00131 0 0.99739 0.00261 0 0.9993 0.0007 0 0.99477 0.00523 0 0.989 0.011 0 0.99885 0.00115 0 0.99872 0.00128 0 0.98977 0.01023 0 0.99478 0.00522 0 0.98966 0.01034 0 0.99472 0.00528 0 0.99918 0.00082 0 0.99891 0.00109 0 0.98986 0.01014 0 0.99932 0.00068 0 0.99937 0.00063 0 0.95955 0.04003 0.00042 1 0 0 0.98806 0.01193 0 0.99872 0.00128 0 0.98045 0.01955 0 0.98225 0.01775 0.00001 0.99747 0.00253 0 0.99479 0.00521 0 0.99747 0.00253 0 0.99935 0.00065 0
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-20:65288 G T 0.99937 0.00063 0 0.99967 0.00033 0 0.99543 0.00457 0 0.97188 0.02812 0 0.9989 0.0011 0 0.0934 0.50382 0.40278 0.8983 0.1006 0.0011 0.04321 0.95679 0 0.99682 0.00318 0 0 0.87952 0.12048 0.99273 0.00727 0 0.98691 0.01309 0 0.88156 0.11843 0.00001 0.15496 0.84473 0.00031 0.90695 0.09165 0.0014 0.99712 0.00288 0 0.97303 0.02691 0.00006 0.99973 0.00027 0 0.92301 0.07572 0.00127 0.99935 0.00065 0 0 0.79449 0.20551 0 1 0 0.00626 0.99374 0 0.99777 0.00223 0 0.97401 0.02599 0 0.82922 0.17076 0.00002 0.99974 0.00026 0 0.99441 0.00559 0 0.79557 0.20435 0.00008 0 1 0 0.65877 0.34123 0 0.99901 0.00099 0 0.99443 0.00557 0 0.96617 0.03383 0 0.0008 0.9992 0 0.00202 0.99739 0.00059 0.89035 0.10777 0.00188 0.99955 0.00045 0 0.97836 0.02164 0 0.99996 0.00004 0 0.00069 0.99919 0.00012 0.76602 0.22148 0.01251 0.00503 0.99497 0 0.9654 0.0346 0 0.88554 0.11121 0.00325 0.9116 0.08839 0.00001 0.42696 0.57304 0 0.55478 0.44522 0 0.36012 0.63988 0
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-20:65900 G A 0 0.00158 0.99842 0 0.00357 0.99643 0 0.00196 0.99804 0 0.01461 0.98539 0 0.00789 0.99211 0 0.01289 0.98711 0 0.96657 0.03343 0 0.00278 0.99722 0 0.00453 0.99547 0.00001 0.99077 0.00923 0.00053 0.05179 0.94768 0 0.00628 0.99372 0 0.9839 0.0161 0 0.0179 0.9821 0 1 0 0 0.00033 0.99967 0 0.00029 0.99971 0 0.00122 0.99878 0.04189 0.95807 0.00003 0 0.0034 0.9966 0 0.99898 0.00102 0 0.00193 0.99807 0.00003 0.99964 0.00032 0 0.01261 0.98738 0 1 0 0.18863 0.7917 0.01967 0 0.00098 0.99902 0 0.99999 0.00001 0 0.17622 0.82378 0 0.00012 0.99988 0 0.08797 0.91203 0 0.00041 0.99959 0 0.00381 0.99619 0 1 0 0.00031 0.02857 0.97112 0 0.00475 0.99525 0 1 0 0 0.00592 0.99408 0 0.99978 0.00022 0 0.00104 0.99896 0.00004 0.99991 0.00005 0.24858 0.74453 0.00688 0.00087 0.0488 0.95033 0 0.07002 0.92998 0.14078 0.85922 0 0.00003 0.98178 0.01819 0 0.02224 0.97776 0 0.13107 0.86893 0 0.00325 0.99675
-20:65951 T C 0.99978 0.00022 0 0.99987 0.00013 0 0.99958 0.00042 0 0.99943 0.00057 0 0.9985 0.0015 0 0.99875 0.00125 0 0.99969 0.00031 0 0.99977 0.00023 0 0.99842 0.00158 0 0.97734 0.02266 0 0.99914 0.00086 0 0.99949 0.00051 0 0.91209 0.0879 0.00001 0.99998 0.00002 0 0.99995 0.00005 0 0.9998 0.0002 0 0.99976 0.00024 0 0.99989 0.00011 0 0.99862 0.00138 0 0.99908 0.00092 0 0.9995 0.0005 0 1 0 0 0.99979 0.00021 0 0.99895 0.00105 0 0.9996 0.0004 0 0.97757 0.02243 0 0.99999 0.00001 0 0.99889 0.00111 0 0.99865 0.00135 0 0.99929 0.00071 0 0.99903 0.00097 0 0.99921 0.00079 0 0.99987 0.00013 0 0.9954 0.0046 0 0.99994 0.00006 0 0.99998 0.00002 0 0.99949 0.00051 0 0.99993 0.00007 0 0.99998 0.00002 0 0.99999 0.00001 0 0 1 0 0.98939 0.01061 0 0.99956 0.00044 0 0.99693 0.00307 0 0.99674 0.00326 0 0.99189 0.00811 0 0.99868 0.00132 0 0.99462 0.00538 0 0.99994 0.00006 0
-20:66370 G A 0 0.00042 0.99958 0 0.00131 0.99869 0 0.0015 0.9985 0.00003 0.01362 0.98635 0 0.00066 0.99934 0 0.01091 0.98909 0 0.98755 0.01245 0 0.00207 0.99793 0 0.00387 0.99613 0 0.44386 0.55614 0 0.03242 0.96758 0 0.00523 0.99477 0 0.54913 0.45087 0 0.00514 0.99486 0 0.99717 0.00283 0 0.00085 0.99915 0 0.00169 0.99831 0 0.00019 0.99981 0 1 0 0 0.00064 0.99936 0.00432 0.99027 0.00541 0 0.00046 0.99954 0.00035 0.99965 0 0 0.00057 0.99943 0.00001 0.99999 0 0 0.62493 0.37507 0 0.00111 0.99889 0.00313 0.99624 0.00063 0 0.11916 0.88084 0 0.00183 0.99817 0 0.04289 0.95711 0 0.00022 0.99978 0 0.00136 0.99864 0.00115 0.75175 0.2471 0 0.00444 0.99556 0 0.0006 0.9994 0.00202 0.75381 0.24417 0 0.00491 0.99509 0 0.99877 0.00123 0 0.00113 0.99887 0 0.00145 0.99855 0.14463 0.64413 0.21124 0 0.01909 0.98091 0.00007 0.05355 0.94638 0 1 0 0.00131 0.73522 0.26347 0 0.00681 0.99319 0 0.05635 0.94365 0 0.0035 0.9965
-20:67398 G C 0.98468 0.01532 0 0.99226 0.00774 0 0.99611 0.00389 0 0.98464 0.01536 0 0.99226 0.00774 0 0.96612 0.03357 0.0003 0.98445 0.01555 0 0.98518 0.01482 0 0.99808 0.00192 0 0.99815 0.00185 0 0.99226 0.00774 0 0.9696 0.03016 0.00024 0.98329 0.01671 0 0.99902 0.00098 0 0.96792 0.03182 0.00027 0.99904 0.00096 0 0.96947 0.03029 0.00024 0.99809 0.00191 0 0.98376 0.01624 0 0.98461 0.01539 0 0.99617 0.00383 0 0.98269 0.01731 0 0.9958 0.0042 0 0.99608 0.00392 0 0.99221 0.00779 0 0.99817 0.00183 0 0.98465 0.01535 0 0.96774 0.03199 0.00027 0.99607 0.00393 0 0.99124 0.00876 0 0.996 0.004 0 0.96971 0.03005 0.00024 0.99227 0.00773 0 0 0.99995 0.00005 0.99903 0.00097 0 0.99217 0.00783 0 0.984 0.016 0 0.99228 0.00772 0 0.99175 0.00825 0 0.9961 0.0039 0 0.96271 0.03705 0.00024 0.98398 0.01602 0 0.98366 0.01634 0 0.98581 0.01419 0 0.96732 0.03241 0.00028 0.99897 0.00103 0 0.99903 0.00097 0 0.96921 0.03055 0.00025 0.98459 0.01541 0
-20:68749 T C 0 0.00393 0.99607 0.00247 0.99753 0 0.00068 0.33889 0.66043 0.00129 0.99783 0.00089 0.89205 0.10795 0 0 0.99908 0.00092 0 0.99834 0.00166 0 0.05938 0.94062 0 0.11921 0.88079 0 0.10624 0.89376 0.03087 0.96913 0 0 0.01545 0.98455 0.66078 0.33922 0 0 1 0 0.67234 0.32766 0 0.66034 0.33966 0 0 0.11694 0.88306 0 0.10717 0.89283 0 0.19779 0.80221 0.00134 0.99732 0.00134 0 0.19239 0.80761 0 0.0077 0.9923 0 0.99852 0.00148 0 0.11693 0.88307 0.00005 0.99995 0 0 0.05907 0.94093 0 0.00782 0.99218 0 1 0 0.0017 0.33297 0.66533 0.65772 0.34228 0 0.00101 0.99849 0.0005 0.00027 0.32913 0.6706 0 0.00783 0.99217 0.10858 0.4418 0.44962 0 0.10656 0.89344 0 0.1064 0.8936 0.50995 0.49005 0 0 1 0 0 0.02997 0.97003 0 1 0 0 0.00178 0.99822 0.00015 0.33086 0.66899 0.10772 0.44228 0.45001 0.51238 0.48762 0 0.00052 0.99897 0.00051 0.01584 0.98416 0 0.0002 0.333 0.6668 0 0.99738 0.00262 0 0.00102 0.99898
-20:69094 G A 0.85768 0.14232 0 0.73982 0.26018 0 0.59872 0.4012 0.00008 0.34734 0.48533 0.16733 0.00116 0.99884 0 0.57495 0.42505 0 0 0.26025 0.73975 0 0.08091 0.91909 0.36535 0.47575 0.1589 0 0.14028 0.85972 0.73951 0.26049 0 0.74699 0.25301 0 0.5763 0.42361 0.00009 0 0.40997 0.59003 0 0.57831 0.42169 0.91783 0.08217 0 0.00857 0.99143 0 0.97884 0.02116 0 0.73792 0.26208 0 0.01565 0.58934 0.39501 0 0.39861 0.60139 0.8413 0.1587 0 0 0.40117 0.59883 0 0.99933 0.00067 0 0.04249 0.95751 0 0.07897 0.92103 0.7515 0.2485 0 0.91855 0.08145 0 0.34369 0.48596 0.17035 0.00075 0.99925 0 0.00155 0.99845 0 0.92336 0.07664 0 0.75212 0.24788 0 0.85233 0.14767 0 0 1 0 0 1 0 0 0.14818 0.85182 0.74008 0.25992 0 0.9787 0.0213 0 0.58751 0.41202 0.00047 0.0004 0.99894 0.00065 0.33799 0.48665 0.17535 0.3328 0.48981 0.17739 0.3439 0.48584 0.17026 0.579 0.42082 0.00018 0 0.99751 0.00249 0.59496 0.40479 0.00025 0 0.58816 0.41184 0.00052 0.99856 0.00092
-20:69408 C T 0.84867 0.15133 0.00001 0.95711 0.04289 0 0.72086 0.25623 0.0229 0.72086 0.25623 0.0229 0.95711 0.04289 0 0 0.99976 0.00024 0.91792 0.08208 0 0 0.99927 0.00073 0.72086 0.25623 0.0229 0.91792 0.08208 0 0.91792 0.08208 0 0.8456 0.15429 0.00011 0.84865 0.15133 0.00002 0 0.99888 0.00112 0.00198 0.99802 0 0.95711 0.04289 0 0.95711 0.04289 0 0.95616 0.04384 0 0.91792 0.08208 0 0.84868 0.15131 0.00002 0.91792 0.08208 0 0.91792 0.08208 0 0.98885 0.01115 0 0.72086 0.25623 0.0229 0.91792 0.08208 0 0.91965 0.08035 0 0.91792 0.08208 0 0.84861 0.15132 0.00007 0.95711 0.04289 0 0.00114 0.9983 0.00056 0.00142 0.99787 0.00071 0.72086 0.25623 0.0229 0.91965 0.08035 0 0.91792 0.08208 0 0 0.99938 0.00062 0.91792 0.08208 0 0.95711 0.04289 0 0.97755 0.02245 0 0.95711 0.04289 0 0.72086 0.25623 0.0229 0.84865 0.15132 0.00002 0.84548 0.15429 0.00023 0.91792 0.08208 0 0.84864 0.15132 0.00003 0.84862 0.15134 0.00004 0.91792 0.08208 0 0.97851 0.02149 0 0.00144 0.84807 0.1505 0.00287 0.84683 0.1503
-20:70980 G A 0.99927 0.00073 0 0.98824 0.01176 0 0.98824 0.01176 0 0.99702 0.00298 0 0.99407 0.00593 0 0.97667 0.02319 0.00014 0.98824 0.01176 0 0.9942 0.0058 0 0.99702 0.00298 0 0.99702 0.00298 0 0.98824 0.01176 0 0.99702 0.00298 0 0.97667 0.02319 0.00014 0.99702 0.00298 0 0.99927 0.00073 0 0.99925 0.00075 0 0.97667 0.02319 0.00014 0.9999 0.0001 0 0.98824 0.01176 0 0.99854 0.00146 0 0.99854 0.00146 0 0.99854 0.00146 0 0.99702 0.00298 0 0.99981 0.00019 0 0.98824 0.01176 0 0.99379 0.00621 0 0.99407 0.00593 0 0.97667 0.02319 0.00014 0.99925 0.00075 0 0.98824 0.01176 0 0.99145 0.00855 0 0.98824 0.01176 0 0.97667 0.02319 0.00014 0.99923 0.00077 0 0.99407 0.00593 0 0.97667 0.02319 0.00014 0.99407 0.00593 0 0.98824 0.01176 0 0.99407 0.00593 0 0.99927 0.00073 0 0 0.97692 0.02308 0.97667 0.02319 0.00014 0.98824 0.01176 0 0.98824 0.01176 0 0.99407 0.00593 0 0.99854 0.00146 0 0.99702 0.00298 0 0.98824 0.01176 0 0.99407 0.00593 0
-20:72719 C T 0.96332 0.03668 0 0.92944 0.07056 0 0.86418 0.13082 0.005 0.96332 0.03668 0 0.98128 0.01872 0 0.96332 0.03668 0 0.96332 0.03668 0 0.92944 0.07056 0 0.86418 0.13082 0.005 0.92943 0.07057 0 0.92942 0.07055 0.00002 0.98128 0.01872 0 0.92943 0.07057 0 0.99032 0.00968 0 0.96332 0.03668 0 0.00728 0.99272 0 0.92942 0.07057 0.00001 0.98128 0.01872 0 0.98128 0.01872 0 0.96332 0.03668 0 0.96332 0.03668 0 0.86418 0.13082 0.005 0.86418 0.13082 0.005 0.00266 0.9973 0.00004 0.96332 0.03668 0 0.99522 0.00478 0 0.99533 0.00467 0 0 1 0 0.92942 0.07057 0.00001 0.96332 0.03668 0 0.99074 0.00926 0 0.96332 0.03668 0 0.99074 0.00926 0 0.92944 0.07056 0 0.86418 0.13082 0.005 0.86418 0.13082 0.005 0.9817 0.0183 0 0.96332 0.03668 0 0.01448 0.98552 0 0.9817 0.0183 0 0.92943 0.07057 0 0.86418 0.13082 0.005 0.92943 0.07057 0 0.96332 0.03668 0 0.92942 0.07057 0.00001 0.99533 0.00467 0 0.92944 0.07056 0 0.92943 0.07057 0 0.86418 0.13082 0.005
-20:72892 G A 0.9996 0.0004 0 0.97494 0.02506 0 0.98728 0.01272 0 0.97494 0.02506 0 0.9992 0.0008 0 0.99359 0.00641 0 0.95063 0.04874 0.00063 0.99359 0.00641 0 0.99677 0.00323 0 0.97494 0.02506 0 0.98728 0.01272 0 0.99359 0.00641 0 0.99359 0.00641 0 0.99677 0.00323 0 0.99842 0.00158 0 0.99685 0.00315 0 0.98728 0.01272 0 0.97494 0.02506 0 0.99919 0.00081 0 0.97494 0.02506 0 0.98728 0.01272 0 0.99838 0.00162 0 0.99662 0.00338 0 0.99359 0.00641 0 0.99359 0.00641 0 0.99685 0.00315 0 0.99359 0.00641 0 0.99677 0.00323 0 0.99685 0.00315 0 0.97494 0.02506 0 0.99685 0.00315 0 0.99917 0.00083 0 0.99359 0.00641 0 0.98728 0.01272 0 0.99685 0.00315 0 0.99359 0.00641 0 0.99677 0.00323 0 0.99919 0.00081 0 0.9999 0.0001 0 0.9992 0.0008 0 0 1 0 0.95063 0.04874 0.00063 0.98757 0.01243 0 0.99677 0.00323 0 0.97494 0.02506 0 0.99685 0.00315 0 0 0.95146 0.04854 0.98728 0.01272 0 0.99359 0.00641 0
-20:73857 G A 0.99901 0.00099 0 0.9961 0.0039 0 0.96965 0.0301 0.00026 0.99224 0.00776 0 0.99619 0.00381 0 0.98466 0.01534 0 0.99619 0.00381 0 0.99987 0.00013 0 0.99224 0.00776 0 0.99987 0.00013 0 0.99804 0.00196 0 0.99901 0.00099 0 0.98466 0.01534 0 0.96965 0.0301 0.00026 0.99224 0.00776 0 0.99224 0.00776 0 0.98466 0.01534 0 0.998 0.002 0 0.98466 0.01534 0 0.99225 0.00775 0 0.96965 0.0301 0.00026 0.96965 0.0301 0.00026 0 0.99998 0.00002 0.98466 0.01534 0 0.99804 0.00196 0 0.9961 0.0039 0 0.99242 0.00758 0 0.98466 0.01534 0 0.9961 0.0039 0 0.96965 0.0301 0.00026 0.9961 0.0039 0 0.99804 0.00196 0 0.99901 0.00099 0 0.98466 0.01534 0 0.9961 0.0039 0 0.96965 0.0301 0.00026 0.9961 0.0039 0 0.99224 0.00776 0 0.9961 0.0039 0 0.96965 0.0301 0.00026 0.99224 0.00776 0 0.98466 0.01534 0 0.96965 0.0301 0.00026 0.99224 0.00776 0 0.98466 0.01534 0 0.96965 0.0301 0.00026 0.96965 0.0301 0.00026 0.99224 0.00776 0 0.9961 0.0039 0
-20:74347 G A 0.00116 0.99884 0 0 0.99938 0.00062 0.80702 0.19298 0 0.8453 0.1547 0 0 0.01035 0.98965 0.97107 0.02893 0 0 0.6389 0.3611 0 0.99751 0.00249 0.93465 0.06535 0 0 1 0 0.99853 0.00147 0 0.7213 0.2786 0.0001 0.0103 0.6929 0.2968 0.00922 0.99078 0 0.00057 0.99526 0.00417 0.99984 0.00016 0 0.00032 0.62687 0.37281 0.99678 0.00322 0 0.55697 0.44246 0.00056 0.99219 0.00781 0 0.87531 0.12469 0 0.9637 0.0363 0 0 0.20695 0.79305 0.94102 0.05898 0 0 0.99997 0.00003 0.99946 0.00054 0 0.99902 0.00098 0 0.73346 0.26654 0 0.87611 0.12389 0 0.94114 0.05886 0 0.60875 0.38858 0.00267 0.00097 0.99903 0 0.00064 0.99892 0.00044 0.81891 0.18109 0 0.96754 0.03246 0 0 1 0 0 0.56625 0.43375 0.9825 0.0175 0 0 0.99998 0.00002 0.99968 0.00032 0 0.91928 0.08072 0 0.93233 0.06767 0 0.78011 0.21989 0 0.87927 0.12044 0.00029 0.94901 0.05099 0 0.98796 0.01204 0 0.99796 0.00204 0 0.99861 0.00139 0 0.99035 0.00965 0
-20:75254 C A 0.11573 0.88427 0 0 0.99994 0.00006 0.00509 0.99491 0 0.06463 0.93526 0.00011 0.99986 0.00014 0 0 1 0 0.80955 0.19044 0 0.99271 0.00729 0 0.82154 0.17846 0 0.96551 0.03449 0 0 0.19296 0.80704 0.04257 0.95743 0 0.77565 0.22435 0 0.79981 0.20019 0 0.89324 0.10676 0 0 0.33007 0.66993 0.88789 0.11211 0 0 0.20067 0.79933 0.87025 0.12975 0 0.00055 0.99816 0.00129 0.70662 0.29338 0 0.00092 0.99789 0.00119 0.99616 0.00384 0 0.81234 0.18766 0 0 1 0 0 0.03111 0.96889 0 0.06146 0.93854 0 0.9951 0.0049 0 1 0 0.89388 0.10612 0 0.85302 0.14698 0 0.98573 0.01427 0 0.68735 0.31265 0 0.70054 0.29946 0 0.97264 0.02736 0 0.93808 0.06192 0 0.99616 0.00384 0 0 1 0 0.00834 0.99166 0 0 0.00866 0.99134 0.83169 0.16831 0 0.8222 0.1778 0 0.02799 0.97201 0 0 0.30711 0.69289 0 0.2486 0.7514 0 0.99416 0.00584 0 0.061 0.939 0.94919 0.05081 0 0 1 0
-20:76962 T C 0 0.0194 0.9806 0 0.00929 0.99071 0 1 0 0 0.08754 0.91245 0 0.00093 0.99907 0 0.00568 0.99432 0 0.01653 0.98347 0 0.03767 0.96233 0 0.0114 0.9886 0 0.00121 0.99879 0 0.00137 0.99863 0 0.01179 0.98821 0 0.00918 0.99082 0 0.00502 0.99498 0 0.01914 0.98086 0 0.04305 0.95695 0 0.06366 0.93634 0 0.00562 0.99438 0 0.00963 0.99037 0 0.0057 0.9943 0.00001 0.08301 0.91698 0 0.9984 0.0016 0 0.0023 0.9977 0 0.98784 0.01216 0 0.06953 0.93047 0 0.00587 0.99413 0.00001 0.0838 0.91619 0 0.01091 0.98909 0 0.00147 0.99853 0.00717 0.15442 0.8384 0 0.00535 0.99465 0 0.03656 0.96344 0 0.01923 0.98077 0.00287 0.99713 0 0.00016 0.99607 0.00377 0 0.03688 0.96312 0 0.00793 0.99207 0.0078 0.15997 0.83223 0 0.01895 0.98105 0 0.00292 0.99708 0 0.02209 0.97791 0.00695 0.15267 0.84038 0 0.01129 0.98871 0.00001 0.08679 0.9132 0.00712 0.15387 0.83901 0 1 0 0 0.0114 0.9886 0 0.02244 0.97756 0 0.00596 0.99404
-20:77013 C T 0.99578 0.00422 0 0.97115 0.02884 0 0 0.96201 0.03799 0.99474 0.00526 0 0.99995 0.00005 0 0 0.96833 0.03167 0.98408 0.01592 0 0.99573 0.00427 0 0.99757 0.00243 0 0.99899 0.00101 0 0.99222 0.00778 0 0.97778 0.02222 0 0.99601 0.00399 0 0.98394 0.01606 0 0.99897 0.00103 0 0.99196 0.00804 0 0.96933 0.03067 0 0.99178 0.00822 0 0.97814 0.02186 0 0.9979 0.0021 0 0.98077 0.01923 0 0.99861 0.00139 0 0.98441 0.01559 0 0.99866 0.00134 0 0.96931 0.03068 0 0.98304 0.01696 0 0.99579 0.00421 0 0.99873 0.00127 0 0.01291 0.98709 0 0.99554 0.00446 0 0.96309 0.03691 0 0.99893 0.00107 0 0.9989 0.0011 0 0.96287 0.03711 0.00001 0.99934 0.00066 0 0.99591 0.00409 0 0.94134 0.05774 0.00092 0.99506 0.00494 0 0.98412 0.01588 0 0.98372 0.01628 0 0.97854 0.02146 0 0.92409 0.07454 0.00137 0.96514 0.03485 0.00002 0.98019 0.01981 0 0.98299 0.01701 0 0.98041 0.01959 0 0.99142 0.00858 0 0.97892 0.02108 0 0.99743 0.00257 0
-20:77816 G A 0.99805 0.00195 0 0.999 0.001 0 0.98248 0.01752 0 0 0.96616 0.03384 0.99908 0.00092 0 0.99518 0.00482 0 0.98367 0.01633 0 0.99884 0.00116 0 0.99889 0.00111 0 0.97964 0.02036 0 0.99686 0.00314 0 0.99767 0.00233 0 0.97999 0.02001 0 0.95746 0.04254 0 0.99943 0.00057 0 0.98702 0.01298 0 0.99554 0.00446 0 0.9935 0.0065 0 0.98128 0.01872 0 0.99632 0.00368 0 0.98228 0.01772 0 0.99882 0.00118 0 0.98362 0.01638 0 0.99548 0.00452 0 0 1 0 0.99671 0.00329 0 0.98713 0.01287 0 0.98339 0.01661 0 0.99143 0.00857 0 0.98345 0.01655 0 0.0187 0.9813 0 0.99533 0.00467 0 0.98286 0.01714 0 0.99886 0.00114 0 0.99566 0.00434 0 0.92368 0.07473 0.00159 0.99187 0.00813 0 0.99186 0.00814 0 0.98323 0.01677 0 0.99832 0.00168 0 0.99048 0.00952 0 0.9651 0.0349 0 0.99974 0.00026 0 0.98399 0.01601 0 0.94695 0.05223 0.00082 0.99781 0.00219 0 0.9933 0.0067 0 0.99762 0.00238 0 0.99584 0.00416 0
-20:79234 T C 0.89997 0.10003 0 0 1 0 0.00058 0.99884 0.00058 0.52659 0.47341 0 0.92331 0.07669 0 0 0.36709 0.63291 0.58106 0.41894 0 0 0.99974 0.00026 0.27055 0.49863 0.23082 0 1 0 0 0.1043 0.8957 0.24882 0.51376 0.23742 0.33395 0.48335 0.18269 0.00305 0.58604 0.41091 0.00071 0.99914 0.00015 0.00057 0.48539 0.51404 0.35414 0.46971 0.17615 0 0.31932 0.68068 0.90253 0.09747 0 0.00068 0.50837 0.49095 0.51868 0.48132 0 0.66721 0.33279 0 0.00257 0.99743 0 0.51375 0.48625 0 0.25479 0.50059 0.24462 0.00014 0.47551 0.52435 0.23427 0.49075 0.27499 0.49787 0.50213 0 0.69349 0.30651 0 0.27751 0.49704 0.22545 0.69763 0.30237 0 0.32122 0.49386 0.18492 0 0.99874 0.00126 0.272 0.49796 0.23004 0.00014 0.4972 0.50266 0.02252 0.97748 0 0.73571 0.26429 0 0 0.20324 0.79676 0.28625 0.52277 0.19098 0.00014 0.47641 0.52345 0.26749 0.49933 0.23318 0.52078 0.47922 0 0.25555 0.50746 0.23699 0.23957 0.49465 0.26578 0.23934 0.49403 0.26663 0.25252 0.49856 0.24892 0.00014 0.47612 0.52374 0.01448 0.98552 0 0.24355 0.50446 0.25199
-20:80071 G A 0 0.9945 0.0055 0 0.99958 0.00042 0.56016 0.4396 0.00024 0.31354 0.49266 0.1938 0.78624 0.21376 0 0.00055 0.56964 0.42982 0.92157 0.07843 0 0.91865 0.08135 0 0.28764 0.49647 0.21589 0.00105 0.99895 0 0 0.33349 0.66651 0.89543 0.10457 0 0.36985 0.47389 0.15625 0.3391 0.49301 0.1679 0.58267 0.41708 0.00026 0 0.20294 0.79706 0.9215 0.0785 0 0 0.33287 0.66713 0.95125 0.04875 0 0 0.35439 0.64561 0.00156 0.99844 0 0 1 0 0.00159 0.99841 0 0.26905 0.5 0.23095 0 0.11857 0.88143 0 0.49071 0.50929 0 0.1088 0.8912 0.00048 0.99805 0.00147 0.00106 0.99894 0 0.00019 0.53817 0.46164 0.71964 0.28036 0 0.58123 0.41869 0.00009 0.84107 0.15893 0 0.00029 0.99915 0.00056 0.90594 0.09406 0 0 0.99423 0.00577 0.76033 0.23967 0 0.67704 0.32296 0 0.00054 0.99815 0.00132 0 0.32849 0.67151 0.90336 0.09664 0 0.01604 0.98352 0.00044 0 0.53843 0.46157 0.25646 0.49446 0.24909 0 0.20565 0.79435 0.00044 0.99711 0.00245 0.00015 0.49118 0.50867 0.6964 0.3036 0 0.25915 0.50367 0.23717
-20:80481 G C 0.98543 0.01457 0 0.98543 0.01457 0 0.97136 0.02864 0 0.97137 0.02863 0 0.99265 0.00735 0 0.94369 0.05548 0.00083 0.99265 0.00735 0 0.99907 0.00093 0 0.98543 0.01457 0 0.99909 0.00091 0 0.99814 0.00186 0 0.99265 0.00735 0 0.94369 0.05548 0.00083 0.99909 0.00091 0 0.99638 0.00362 0 0.97136 0.02864 0 0.98543 0.01457 0 0.99994 0.00006 0 0.99638 0.00362 0 0.99909 0.00091 0 0.99818 0.00182 0 0.99909 0.00091 0 0.99907 0.00093 0 0.99818 0.00182 0 0.99818 0.00182 0 0.99818 0.00182 0 0.99818 0.00182 0 0.98543 0.01457 0 0.99907 0.00093 0 0.99638 0.00362 0 0.99977 0.00023 0 0.98543 0.01457 0 0.99818 0.00182 0 0.98543 0.01457 0 0.94911 0.05089 0 0.98543 0.01457 0 0.99282 0.00718 0 0.99265 0.00735 0 0.99818 0.00182 0 0.99818 0.00182 0 0 1 0 0.94369 0.05548 0.00083 0.97137 0.02863 0 0.97136 0.02864 0 0.97137 0.02863 0 0.99265 0.00735 0 0 1 0 0.99638 0.00362 0 0.99265 0.00735 0
-20:80655 A G 0 0.00516 0.99484 0.00165 0.07731 0.92104 0 0.02068 0.97932 0 0.00516 0.99484 0 0.02068 0.97932 0 0.02068 0.97932 0 0.02068 0.97932 0 0.00266 0.99734 0 0.01047 0.98953 0 0.00133 0.99867 0 0.00133 0.99867 0 0.00528 0.99472 0 0.0404 0.9596 0 0.02068 0.97932 0 0.00278 0.99722 0 0.00516 0.99484 0.00165 0.07731 0.92104 0 0.00033 0.99967 0.07709 0.92291 0 0 0.01047 0.98953 0 0.02068 0.97932 0 1 0 0 0.00259 0.99741 0.00165 0.07731 0.92104 0.00165 0.07731 0.92104 0 0.0404 0.9596 0 0.02068 0.97932 0 0.02068 0.97932 0 0.00516 0.99484 0 0.00271 0.99729 0 0.0404 0.9596 0 0.0404 0.9596 0 0.00259 0.99741 0.00018 0.99982 0 0 0.00067 0.99933 0 0.01047 0.98953 0 0.01047 0.98953 0 0.00259 0.99741 0 0.00017 0.99983 0 0.00516 0.99484 0 0.00516 0.99484 0.00165 0.07731 0.92104 0 0.00528 0.99472 0 0.02068 0.97932 0.00165 0.07731 0.92104 0 0.02068 0.97932 0 0.00259 0.99741 0 0.01047 0.98953 0 0.00516 0.99484
-20:80728 C G 0.99568 0.00432 0 0.99121 0.00879 0 0.99557 0.00443 0 0 0.99999 0.00001 0.98261 0.01739 0 0.96561 0.03408 0.0003 0.96561 0.03408 0.0003 0.99557 0.00443 0 0.99121 0.00879 0 0.99121 0.00879 0 0.99121 0.00879 0 0.99121 0.00879 0 0.99568 0.00432 0 0.99121 0.00879 0 0.98261 0.01739 0 0.96561 0.03408 0.0003 0.99557 0.00443 0 0.99783 0.00217 0 0.99121 0.00879 0 0.98261 0.01739 0 0.98261 0.01739 0 0.99944 0.00056 0 0.99557 0.00443 0 0.96561 0.03408 0.0003 0.99121 0.00879 0 0.99121 0.00879 0 0.99121 0.00879 0 0.99121 0.00879 0 0.99121 0.00879 0 0.99121 0.00879 0 0.96561 0.03408 0.0003 0.99557 0.00443 0 0.96561 0.03408 0.0003 0.98261 0.01739 0 0.99783 0.00217 0 0.99121 0.00879 0 0.99557 0.00443 0 0.99891 0.00109 0 0.99783 0.00217 0 0.99888 0.00112 0 0.99945 0.00055 0 0.96561 0.03408 0.0003 0.99783 0.00217 0 0.99121 0.00879 0 0.98261 0.01739 0 0.99121 0.00879 0 0.99973 0.00027 0 0.96561 0.03408 0.0003 0.99121 0.00879 0
-20:81666 C T 0.99491 0.00509 0 0.98006 0.01994 0 0.9899 0.0101 0 0.9975 0.0025 0 0.98006 0.01994 0 0.96061 0.03898 0.00041 0.96061 0.03898 0.00041 0.98006 0.01994 0 0.96061 0.03898 0.00041 0.96061 0.03898 0.00041 0.96061 0.03898 0.00041 0.98006 0.01994 0 0.98006 0.01994 0 0.99491 0.00509 0 0.98006 0.01994 0 0.99491 0.00509 0 0.9899 0.0101 0 0 0.85924 0.14076 0.99503 0.00497 0 0.96061 0.03898 0.00041 0.98006 0.01994 0 0.9899 0.0101 0 0.98005 0.01994 0 0.98547 0.01453 0 0.93696 0.06304 0 0.98006 0.01994 0 0.98006 0.01994 0 0.99491 0.00509 0 0.99479 0.00521 0 0.9899 0.0101 0 0.98006 0.01994 0 0.98005 0.01994 0 0.98006 0.01994 0 0.98006 0.01994 0 0.98005 0.01994 0 0.98006 0.01994 0 0.99491 0.00509 0 0.9975 0.0025 0 0.98005 0.01994 0 0.98006 0.01994 0 0.99937 0.00063 0 0.96061 0.03898 0.00041 0.99491 0.00509 0 0.98005 0.01994 0 0.98005 0.01994 0 0.9899 0.0101 0 0.98006 0.01994 0 0.98006 0.01994 0 0.98005 0.01994 0
-20:81979 T C 0.67264 0.29453 0.03284 0.00254 0.99741 0.00004 0.67264 0.29453 0.03284 0.81919 0.18035 0.00046 0.81957 0.18043 0 0.81954 0.18046 0 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.90046 0.09954 0 0.67264 0.29453 0.03284 0.81953 0.18045 0.00001 0.67264 0.29453 0.03284 0.90046 0.09954 0 0.67264 0.29453 0.03284 0.81565 0.18375 0.00059 0.81953 0.18045 0.00001 0.67264 0.29453 0.03284 0.90046 0.09954 0 0.94748 0.05252 0 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.90046 0.09954 0 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.04709 0.95284 0.00008 0 0.69141 0.30859 0.67264 0.29453 0.03284 0.81957 0.18043 0 0.81948 0.18041 0.00011 0.81957 0.18043 0 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.94748 0.05252 0 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.81953 0.18045 0.00001 0.90046 0.09954 0 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.00625 0.8151 0.17865 0.67264 0.29453 0.03284 0.67264 0.29453 0.03284 0.98624 0.01376 0 0.00046 0.99954 0
-20:82079 G A 0.94877 0.05123 0 0.94763 0.05237 0 0.90081 0.09918 0.00001 0.94763 0.05237 0 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.9008 0.09919 0.00001 0 0.90122 0.09878 0.9008 0.09919 0.00001 0 0.81746 0.18254 0.0313 0.9687 0 0.94648 0.05352 0 0.81203 0.17798 0.00999 0.00972 0.99017 0.00012 0.90079 0.09919 0.00002 0.94763 0.05237 0 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.94648 0.05352 0 0.9008 0.09919 0.00001 0.81203 0.17798 0.00999 0.97304 0.02696 0 0.97304 0.02696 0 0.81203 0.17798 0.00999 0.89866 0.10126 0.00008 0.9008 0.09919 0.00001 0.90081 0.09918 0.00001 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.94763 0.05237 0 0.97244 0.02756 0 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.9008 0.09919 0.00001 0.81203 0.17798 0.00999 0.90079 0.09919 0.00002 0.97304 0.02696 0 0.81203 0.17798 0.00999 0.81203 0.17798 0.00999 0.97244 0.02756 0 0.94763 0.05237 0 0.90077 0.09919 0.00004 0.90081 0.09918 0.00001 0.99324 0.00676 0 0.9866 0.0134 0
-20:82215 G A 0.98576 0.01424 0 0.89724 0.10276 0 0.89716 0.10284 0 0.66329 0.30211 0.03461 0.90676 0.09324 0 0 0.68306 0.31694 0.94686 0.05314 0 0.89718 0.10282 0 0.94687 0.05313 0 0.97198 0.02802 0 0.17372 0.82602 0.00026 0.89731 0.10269 0 0.81408 0.18588 0.00003 0.66327 0.30212 0.03461 0.81402 0.18593 0.00005 0 0.68821 0.31179 0.81394 0.18603 0.00003 0.66337 0.30204 0.03459 0.66327 0.30212 0.03461 0.81397 0.18598 0.00005 0.66363 0.30184 0.03453 0.81368 0.18597 0.00035 0.89716 0.10284 0 0.66327 0.30212 0.03461 0 0.81467 0.18533 0.66327 0.30212 0.03461 0.81393 0.18602 0.00005 0 0.99815 0.00185 0.66332 0.30208 0.0346 0.89716 0.10284 0 0.81394 0.18598 0.00008 0.66335 0.30206 0.03459 0.67784 0.29082 0.03134 0.66327 0.30212 0.03461 0.66327 0.30212 0.03461 0.66328 0.30211 0.03461 0.66329 0.3021 0.03461 0.81392 0.18601 0.00007 0.81392 0.186 0.00008 0.81392 0.18601 0.00007 0 0.99768 0.00232 0.81395 0.18597 0.00008 0.66329 0.30211 0.03461 0.66335 0.30206 0.03459 0.00156 0.99731 0.00114 0.97199 0.02801 0 0.80978 0.18932 0.0009 0.94568 0.05432 0 0.81392 0.18602 0.00005
-20:82217 G A 0 0.01364 0.98636 0.00001 0.17921 0.82078 0.30225 0.69775 0 0.03228 0.29337 0.67435 0 0.16487 0.83513 0 0.09676 0.90324 0 0.05324 0.94676 0.00004 0.17929 0.82067 0 0.05209 0.94791 0 0.02684 0.97316 0 0.09881 0.90119 0 0.09867 0.90133 0.00002 0.17922 0.82076 0.03228 0.29338 0.67434 0 0.17922 0.82078 0 0.09674 0.90326 0 0.1793 0.8207 0.03227 0.29331 0.67442 0.03228 0.29338 0.67433 0 0.17929 0.82071 0.03222 0.29312 0.67466 0.17782 0.81763 0.00455 0 0.0988 0.9012 0.03228 0.29338 0.67433 0 0.1793 0.8207 0 0.09881 0.90119 0 0.1793 0.8207 0 0.05209 0.94791 0.03227 0.29334 0.67439 0.00014 0.99201 0.00785 0 0.17929 0.82071 0 0.17926 0.82074 0.02986 0.28288 0.68725 0.03228 0.29338 0.67433 0.03228 0.29338 0.67434 0.17841 0.82045 0.00114 0.03228 0.29337 0.67436 0.17265 0.8123 0.01505 0.00001 0.17932 0.82066 0 0.1793 0.8207 0 0.0988 0.9012 0 0.17928 0.82072 0.03228 0.29337 0.67435 0.03227 0.29332 0.67441 0 0.09878 0.90122 0 0.99954 0.00046 0 0.10083 0.89917 0.00028 0.99972 0 0.00001 0.17932 0.82067
-20:82701 T C 0.00425 0.82671 0.16904 0.90653 0.09347 0 0 0.99993 0.00007 0.68845 0.28247 0.02908 0.99417 0.00583 0 0.82933 0.17066 0.00001 0.90646 0.09354 0 0.95085 0.04915 0 0.82937 0.17063 0 0.97529 0.02471 0 0.90646 0.09354 0 0.95091 0.04909 0 0.90654 0.09346 0 0.95084 0.04916 0 0.90651 0.09349 0 0.8294 0.1706 0 0.90646 0.09354 0 0.97472 0.02528 0 0.82933 0.17067 0 0 0.7102 0.2898 0.90657 0.09343 0 0 0.71004 0.28996 0.97529 0.02471 0 0 1 0 0.00487 0.99513 0 0.00243 0.82798 0.16959 0.90647 0.09353 0 0 0.99983 0.00017 0 1 0 0.95084 0.04916 0 0.82934 0.17065 0.00001 0.95085 0.04915 0 0.98805 0.01195 0 0 1 0 0.90646 0.09354 0 0.90647 0.09353 0 0.90647 0.09353 0 0.97529 0.02471 0 0.95192 0.04808 0 0.04955 0.95045 0 0.99682 0.00318 0 0.82938 0.17062 0 0.02701 0.81075 0.16224 0.90649 0.09351 0 0.82941 0.17059 0 0.95085 0.04915 0 0.82938 0.17061 0.00001 0.95084 0.04916 0 0.82936 0.17064 0
-20:87112 G A 0 0.98682 0.01318 0 0.09144 0.90856 0.82971 0.17029 0 0.64195 0.35796 0.00009 0 0.05628 0.94372 0.4237 0.57508 0.00122 0.70618 0.26068 0.03314 0 0.99853 0.00147 0.13433 0.46371 0.40196 0.90424 0.09576 0 0 1 0 0.00029 0.99866 0.00105 0.53234 0.40476 0.0629 0.88761 0.11239 0 0.39151 0.60836 0.00013 0 0.42284 0.57716 0.4774 0.52247 0.00013 0 0.01147 0.98853 0.90922 0.09078 0 0 0.15293 0.84707 0 1 0 0.94932 0.05068 0 0.39581 0.60384 0.00035 0.98181 0.01819 0 0.91391 0.08609 0 0 0.99346 0.00654 0 0.02486 0.97514 0.9044 0.0956 0 0.48358 0.51587 0.00055 0 1 0 0 0.29412 0.70588 0.71414 0.28586 0 0 0.28661 0.71339 0.96528 0.03472 0 0.00114 0.99886 0 0.7923 0.2076 0.0001 0.67152 0.28943 0.03905 0.00039 0.99961 0 0.69536 0.30464 0 0.41007 0.58035 0.00958 0.00027 0.99973 0 0.75396 0.24592 0.00012 0.25434 0.49315 0.25251 0.57316 0.42646 0.00037 0 0.43744 0.56256 0 1 0 0.00007 0.28249 0.71744 0.46047 0.47107 0.06846 0 0.09776 0.90224
-20:87416 A C 0 0.08263 0.91737 0 0.05169 0.94831 0.53385 0.46603 0.00012 0.37806 0.61892 0.00303 0 0.00489 0.99511 0 0.26736 0.73264 0.87678 0.12322 0 0 0.99708 0.00292 0 0.14412 0.85588 0.87385 0.12615 0 0.06792 0.70866 0.22342 0.14738 0.85244 0.00018 0.39313 0.48694 0.11993 0.87626 0.12374 0 0.00036 0.69739 0.30225 0.01996 0.22602 0.75402 0.19095 0.66054 0.14851 0 0.02073 0.97927 0.9764 0.0236 0 0 0.07168 0.92832 0.08389 0.63091 0.2852 0.00162 0.99774 0.00064 0.00111 0.99865 0.00024 0 0.18666 0.81334 0.19468 0.64743 0.15789 0.00035 0.96124 0.03841 0 0.02586 0.97414 0.65379 0.34621 0 0.0002 0.4278 0.572 0.552 0.448 0 0.00031 0.99969 0 0.00044 0.99936 0.0002 0.02169 0.23215 0.74616 0 0.57515 0.42485 0.00078 0.99922 0 0.56503 0.36838 0.06659 0.74559 0.25438 0.00003 0.00014 0.99889 0.00097 0.00481 0.99519 0 0.00005 0.38976 0.6102 0 0.07312 0.92688 0.4179 0.46142 0.12068 0.0712 0.44865 0.48016 0.12972 0.53123 0.33905 0 0.08238 0.91762 0.29856 0.70144 0 0 0.0491 0.9509 0.52781 0.47219 0 0.00089 0.08872 0.91039
-20:88155 T C 0.99873 0.00127 0 0.99912 0.00088 0 0.99146 0.00854 0 0.99252 0.00748 0 0.99959 0.00041 0 0.97939 0.0205 0.00011 0.99799 0.00201 0 0.9949 0.0051 0 0.99815 0.00185 0 0.99797 0.00203 0 0.99962 0.00038 0 0.99967 0.00033 0 0.99289 0.00711 0 0.99799 0.00201 0 0.99831 0.00169 0 0.99417 0.00583 0 0.99662 0.00338 0 0.9993 0.0007 0 0.96655 0.03307 0.00038 0.99782 0.00218 0 0.99936 0.00064 0 0.99994 0.00006 0 0.99919 0.00081 0 0.99686 0.00314 0 0.99908 0.00092 0 0.99991 0.00009 0 0.99925 0.00075 0 0.99268 0.00732 0 0.99877 0.00123 0 0.99285 0.00715 0 0.9997 0.0003 0 0.99806 0.00194 0 0.99967 0.00033 0 0.99901 0.00099 0 0.99729 0.00271 0 0.99804 0.00196 0 0.98448 0.01552 0 0.99866 0.00134 0 0.99978 0.00022 0 0.99928 0.00072 0 0.99493 0.00507 0 0 0.97476 0.02524 0.99985 0.00015 0 0.98978 0.01022 0 0.99704 0.00296 0 0.99843 0.00157 0 0.99969 0.00031 0 0.99958 0.00042 0 0.99994 0.00006 0
-20:88827 C A 0 1 0 0.99296 0.00704 0 0.78046 0.21954 0 0.51072 0.45827 0.03101 0.9916 0.0084 0 0.00055 0.79883 0.20063 0.969 0.031 0 0.98632 0.01368 0 0.52294 0.39916 0.0779 0.99975 0.00025 0 0 1 0 0.99188 0.00812 0 0.81019 0.17823 0.01158 0.88171 0.11298 0.00531 0.97808 0.02192 0 0 0.99919 0.00081 0.94438 0.05562 0 0.98258 0.01742 0 0.9358 0.06419 0 0.15147 0.82171 0.02682 0.97229 0.02771 0 0.67583 0.32417 0 0.97618 0.02382 0 0 0.35154 0.64846 0.00312 0.99688 0 0.42786 0.53437 0.03777 0.96618 0.03382 0 0 0.99982 0.00018 0.00042 0.82504 0.17454 0.95649 0.04351 0 0.95596 0.04403 0 0.96845 0.03155 0 0.00069 0.99931 0 0.47029 0.52958 0.00013 0.85064 0.14089 0.00847 0.90279 0.09721 0.00001 0.99033 0.00967 0 0.9796 0.0204 0 0 1 0 0 1 0 0.9692 0.0308 0 0.78034 0.20271 0.01695 0 1 0 0.00403 0.99585 0.00012 0.00064 0.99936 0 0.95765 0.04235 0 0.94097 0.05902 0 0.92941 0.07059 0 0.98831 0.01169 0
-20:88924 A T 0.98962 0.01038 0 0.98025 0.01975 0 0.99789 0.00211 0 0.98811 0.01189 0 0.99887 0.00113 0 0.97235 0.0276 0.00005 0.99989 0.00011 0 0.97939 0.02061 0 0.97136 0.02864 0 0.99992 0.00008 0 0.99881 0.00119 0 0.96048 0.03948 0.00003 0.99758 0.00242 0 0.99673 0.00327 0 0.99861 0.00139 0 0.99768 0.00232 0 0.99469 0.00531 0 0.99509 0.00491 0 0.9998 0.0002 0 0.9574 0.04238 0.00022 0.9764 0.0236 0 0.99666 0.00334 0 0.99424 0.00576 0 0.99926 0.00074 0 0.99981 0.00019 0 0.96988 0.03002 0.00009 0.9901 0.0099 0 0.99859 0.00141 0 0.98592 0.01408 0 0.99337 0.00663 0 0.95983 0.04013 0.00004 0.99847 0.00153 0 0.98472 0.01528 0 0.99986 0.00014 0 0.99784 0.00216 0 0.99597 0.00403 0 0.99819 0.00181 0 0.98837 0.01163 0 0.99932 0.00068 0 0.99795 0.00205 0 0 0.85355 0.14645 0.99734 0.00266 0 0.99958 0.00042 0 0.96595 0.03374 0.00031 0.99052 0.00948 0 0.99534 0.00466 0 0.96118 0.03882 0 0.97741 0.02259 0 0.96138 0.03862 0
-20:89802 T C 0.99294 0.00706 0 0.99497 0.00503 0 0.99991 0.00009 0 0.99853 0.00147 0 0 1 0 0.99954 0.00046 0 0.99958 0.00042 0 0.9987 0.0013 0 0.99927 0.00073 0 0.99994 0.00006 0 0.9996 0.0004 0 0.99007 0.00993 0 0.9918 0.0082 0 0.99994 0.00006 0 0.99591 0.00409 0 0.99657 0.00343 0 0.99989 0.00011 0 0.9976 0.0024 0 0.99925 0.00075 0 0.9959 0.0041 0 0.99033 0.00967 0 0.99953 0.00047 0 0.99974 0.00026 0 0.99997 0.00003 0 0.99993 0.00007 0 0.99984 0.00016 0 0.99968 0.00032 0 0.99953 0.00047 0 0.99615 0.00385 0 0.99935 0.00065 0 0.99935 0.00065 0 0.99713 0.00287 0 0.60508 0.39492 0 0.99942 0.00058 0 0.99993 0.00007 0 0.99821 0.00179 0 0.99844 0.00156 0 0.99943 0.00057 0 0.99997 0.00003 0 0.99947 0.00053 0 0.99826 0.00174 0 0.9961 0.0039 0 0.99892 0.00108 0 0.99497 0.00503 0 0.99671 0.00329 0 0.99818 0.00182 0 0.99773 0.00227 0 0.99849 0.00151 0 0.99996 0.00004 0
-20:90008 C A 0.98951 0.01049 0 0.98576 0.01424 0 0.67644 0.32354 0.00003 0.512 0.48796 0.00004 0.99684 0.00316 0 0.6097 0.37944 0.01086 0 0.00547 0.99453 0 1 0 0.98529 0.01471 0 0 0.05583 0.94417 0.99624 0.00376 0 0 0.99904 0.00096 0 0.45435 0.54565 0 0.31964 0.68036 0.00088 0.99912 0 0.95032 0.04968 0 0.00071 0.99929 0 0.98108 0.01892 0 0 1 0 0.99042 0.00958 0 0.8366 0.1634 0 0.99435 0.00565 0 0.01139 0.98861 0 0.9684 0.0316 0 0 0.99997 0.00003 0.66159 0.3384 0.00001 0.96111 0.03889 0 0 1 0 0.55083 0.424 0.02517 0.62627 0.37365 0.00008 0 0.99992 0.00008 0.00048 0.99952 0 0.82579 0.16972 0.00449 0.98572 0.01428 0 0.99674 0.00326 0 0 0.11415 0.88585 0 0.09945 0.90055 0.9413 0.0587 0 0.0052 0.9948 0 0.72199 0.27798 0.00004 0.98853 0.01147 0 0.00039 0.63924 0.36036 0.56838 0.42008 0.01154 0.34535 0.5049 0.14975 0.98343 0.01657 0 0.90569 0.09431 0 0.95953 0.04047 0 0.94878 0.05122 0 0.97953 0.02047 0
-20:90754 A T 0.99993 0.00007 0 0.99858 0.00142 0 0.99811 0.00189 0 0.97757 0.02243 0 0.99723 0.00277 0 0.9831 0.01686 0.00004 0.99845 0.00155 0 0.9989 0.0011 0 0.9773 0.02256 0.00014 0.99812 0.00188 0 0 0.99334 0.00666 0.99463 0.00537 0 0.99633 0.00367 0 0.99904 0.00096 0 0.99522 0.00478 0 0.99561 0.00439 0 0.98946 0.01054 0 0.99997 0.00003 0 0.99341 0.00651 0.00008 0.99736 0.00264 0 0.98449 0.01551 0 0.99954 0.00046 0 0.99709 0.00291 0 0.99959 0.00041 0 0.99618 0.00382 0 0.99806 0.00194 0 0.99903 0.00097 0 0.99915 0.00085 0 0.99697 0.00303 0 0.9917 0.0083 0 0.99999 0.00001 0 0.99948 0.00052 0 0.99769 0.00231 0 0.99246 0.00753 0.00002 0.99823 0.00177 0 0.99978 0.00022 0 0.99978 0.00022 0 0.99762 0.00238 0 0.99646 0.00354 0 0.97338 0.02656 0.00007 0.99973 0.00027 0 0.99476 0.00524 0 0.99871 0.00129 0 0.99093 0.00907 0 0.99853 0.00147 0 0.99582 0.00418 0 0.99236 0.00764 0 0.98218 0.01782 0 0.99812 0.00188 0
-20:90984 A G 0 0.99992 0.00008 0.9681 0.0319 0 0 0.69868 0.30132 0.00766 0.99234 0 0.99654 0.00346 0 0.00013 0.99947 0.0004 0.99275 0.00725 0 0.99775 0.00225 0 0.49158 0.4188 0.08962 0.9839 0.01595 0.00015 0.05179 0.94264 0.00557 0.99218 0.00782 0 0.9773 0.0227 0 0.99699 0.00301 0 0.93997 0.06003 0 0 0.94697 0.05303 0.98313 0.01687 0 0.99651 0.00349 0 0.99773 0.00227 0 0.00027 0.99973 0 0.98606 0.01394 0 0.00067 0.99925 0.00008 0.98538 0.01462 0 0.00036 0.99964 0 0 0.99875 0.00125 0.00047 0.99953 0 0.99868 0.00132 0 0 1 0 0.19092 0.80908 0 0.9998 0.0002 0 0.99482 0.00518 0 0.98576 0.01424 0 0.00007 0.99992 0.00001 0.31505 0.68495 0 0.99889 0.00111 0 0.99673 0.00327 0 0.99586 0.00414 0 0.99232 0.00768 0 0 1 0 0 1 0 0.98536 0.01464 0 0.86067 0.13819 0.00114 0 1 0 0.61111 0.38889 0 0.00002 0.73504 0.26493 0.99841 0.00159 0 0.99051 0.00949 0 0.81234 0.18766 0 0.99129 0.00871 0
-20:91088 C T 0 0.03766 0.96234 0 0.01008 0.98992 0 0.17578 0.82422 0 0.04835 0.95165 0 0.00342 0.99658 0 0.04167 0.95833 0 0.00431 0.99569 0 0.0101 0.9899 0 0.05494 0.94506 0 0.00279 0.99721 0 0.01447 0.98553 0 0.00151 0.99849 0.00026 0.06271 0.93703 0 0.05583 0.94417 0 0.00269 0.99731 0 0.01192 0.98808 0 0.04663 0.95337 0 0.00754 0.99246 0.00008 0.99992 0 0 0.00619 0.99381 0.00013 0.57886 0.42101 0 0.50218 0.49782 0 0.01149 0.98851 0 1 0 0 0.00445 0.99555 0 0.01966 0.98034 0 0.00101 0.99899 0 0.00093 0.99907 0.00657 0.14753 0.8459 0 1 0 0 0.00408 0.99592 0 0.00398 0.99602 0 0.00228 0.99772 0.25296 0.74704 0 0.0005 0.9995 0 0 0.00057 0.99943 0 0.0002 0.9998 0 0.6986 0.3014 0 0.00065 0.99935 0 0.04661 0.95339 0 0.00766 0.99234 0.00149 0.13634 0.86218 0 0.00175 0.99825 0 0.04788 0.95212 0 0.04247 0.95753 0.04729 0.94996 0.00275 0 0.01305 0.98695 0 0.46692 0.53308 0 0.00317 0.99683
-20:91346 G A 0 0.9997 0.0003 0.92193 0.07609 0.00198 0.02558 0.67253 0.30188 0.04532 0.92716 0.02752 0.97132 0.02867 0 0 0.94583 0.05417 0.98215 0.01785 0 0.99775 0.00225 0 0.47838 0.42615 0.09547 0.99036 0.00964 0 0 1 0 0.98113 0.01887 0 0.9769 0.0231 0 0.99703 0.00297 0 0.9258 0.0742 0 0 1 0 0.98117 0.01883 0 0.99486 0.00514 0 0.98699 0.01301 0 0.00083 0.99917 0 0.98791 0.01209 0 0.00007 0.99984 0.00009 0.99403 0.00597 0 0.00002 0.99993 0.00005 0.00003 0.94936 0.05061 0 0.99898 0.00102 0.99941 0.00059 0 0 1 0 0.00256 0.99744 0 0.99702 0.00298 0 0.99017 0.00983 0 0.97618 0.02382 0 0.00027 0.99966 0.00007 0.01797 0.98199 0.00003 0.99579 0.00421 0 0.99162 0.00838 0 0.99515 0.00485 0 0.99234 0.00766 0 0 1 0 0 0.88678 0.11322 0.98965 0.01035 0 0.84887 0.15112 0.00001 0 1 0 0.60337 0.39663 0 0 0.68015 0.31985 0.97579 0.02421 0 0.9865 0.0135 0 0.80096 0.19904 0.00001 0.99762 0.00238 0
-20:91508 G A 0 0.94315 0.05685 0 0.03977 0.96023 0.01702 0.25754 0.72544 0.00001 0.11059 0.8894 0.00001 0.06685 0.93314 0.00851 0.17105 0.82044 0 0.01757 0.98243 0 0.07286 0.92714 0 0.10657 0.89343 0 0.03443 0.96557 0 0.04389 0.95611 0.00001 0.07257 0.92742 0 0.1052 0.8948 0.00763 0.16484 0.82753 0 0.00983 0.99017 0 0.04797 0.95203 0 0.10288 0.89712 0 0.00516 0.99484 0.11545 0.88419 0.00036 0.00582 0.14823 0.84595 0.19428 0.80572 0 0 0.96699 0.03301 0 0.01173 0.98827 0 1 0 0 0.04231 0.95769 0 0.05313 0.94687 0 0.0045 0.9955 0 0.00269 0.99731 0 0.13875 0.86125 0.00008 0.99992 0 0 0.00931 0.99069 0 0.00537 0.99463 0 0.02177 0.97823 0.2719 0.7281 0 0.90559 0.09441 0 0 0.01715 0.98285 0 0.00218 0.99782 0 1 0 0 0.02093 0.97907 0 0.00789 0.99211 0 0.00538 0.99462 0.01326 0.20956 0.77717 0 0.04306 0.95694 0 0.10217 0.89783 0.00938 0.17309 0.81753 0 0.26462 0.73538 0 0.04208 0.95792 0 1 0 0 0.00248 0.99752
-20:91707 C T 0.99123 0.00877 0 0.96527 0.03473 0 0.96527 0.03473 0 0.933 0.067 0 0.96527 0.03473 0 0.933 0.067 0 0.00596 0.99404 0 0.7657 0.21861 0.0157 0.99123 0.00877 0 0.96527 0.03473 0 0.87473 0.12526 0.00001 0.96527 0.03473 0 0.87473 0.12526 0.00001 0 0.87525 0.12475 0 1 0 0.87468 0.12526 0.00006 0.7657 0.21861 0.0157 0.98267 0.01733 0 0 0.77874 0.22126 0.00665 0.99335 0 0.99123 0.00877 0 0.99103 0.00897 0 0.933 0.067 0 0.87473 0.12526 0.00001 0.87473 0.12526 0.00001 0.933 0.067 0 0.7657 0.21861 0.0157 0.99549 0.00451 0 0.98267 0.01733 0 0.96527 0.03473 0 0.98267 0.01733 0 0.96527 0.03473 0 0.93156 0.06844 0 0.99103 0.00897 0 0.933 0.067 0 0.7657 0.21861 0.0157 0 0.9995 0.0005 0.99558 0.00442 0 0.7657 0.21861 0.0157 0.62101 0.37872 0.00026 0.933 0.067 0 0 0.87525 0.12475 0 0.77874 0.22126 0.8747 0.12526 0.00004 0.7657 0.21861 0.0157 0.99123 0.00877 0 0.7657 0.21861 0.0157 0.98267 0.01733 0 0.99946 0.00054 0
-20:91716 C T 0.99898 0.00102 0 0.99197 0.00803 0 0.99587 0.00413 0 0.9688 0.03119 0 0.9841 0.0159 0 0.99197 0.00803 0 0.9841 0.0159 0 0.93876 0.06023 0.00101 0.99801 0.00199 0 0.99197 0.00803 0 0.99197 0.00803 0 0.99605 0.00395 0 0.9688 0.03119 0 0.9841 0.0159 0 0.99898 0.00102 0 0.93876 0.06023 0.00101 0.93876 0.06023 0.00101 0.9841 0.0159 0 0.9688 0.03119 0 0 1 0 0.99577 0.00423 0 0.99801 0.00199 0 0.9688 0.03119 0 0.9688 0.03119 0.00001 0.9688 0.03119 0 0.9688 0.03119 0 0.9688 0.03119 0 0.99197 0.00803 0 0.99595 0.00405 0 0.9841 0.0159 0 0.99605 0.00395 0 0.9841 0.0159 0 0.9841 0.0159 0 0.99797 0.00203 0 0.9841 0.0159 0 0.9841 0.0159 0 0.9841 0.0159 0 0.99197 0.00803 0 0.9841 0.0159 0 0 0.99991 0.00009 0.9688 0.03119 0 0.93876 0.06023 0.00101 0.9688 0.03119 0 0.9841 0.0159 0 0.93876 0.06023 0.00101 0.9841 0.0159 0 0.9841 0.0159 0 0.999 0.001 0 0.99988 0.00012 0
-20:92366 A G 0 0.27992 0.72008 0 0.44279 0.55721 0.37531 0.47454 0.15015 0.76028 0.23972 0 0 0.2846 0.7154 0.37617 0.47424 0.1496 0.61178 0.38822 0 0.00063 0.998 0.00137 0.61178 0.38822 0 0.75481 0.24519 0 0 1 0 0.92759 0.07241 0 0 1 0 0 0.44278 0.55722 0.75903 0.24097 0 0 1 0 0.0004 0.99932 0.00028 0 0.28551 0.71449 0.75859 0.24141 0 0 0.08913 0.91087 0 0.99914 0.00086 0.99026 0.00974 0 0 1 0 0.9623 0.0377 0 0.75869 0.24131 0 0.37503 0.47464 0.15033 0 0.28551 0.71449 0.92594 0.07406 0 0.96234 0.03766 0 0 0.99956 0.00044 0 0.99656 0.00344 0.00206 0.99794 0 0 1 0 0.75902 0.24098 0 0 0.9978 0.0022 0.92759 0.07241 0 0.61173 0.38827 0 0.99026 0.00974 0 0.75869 0.24131 0 0.9276 0.0724 0 0.77968 0.22032 0 0.37766 0.47367 0.14867 0.61185 0.38815 0 0.37757 0.4737 0.14872 0 1 0 0.00623 0.60902 0.38475 0 0.99944 0.00056 0.00079 0.99784 0.00137 0 0.28466 0.71534
-20:92527 A G 0 0.03293 0.96707 0 0.01718 0.98282 0.00089 0.99764 0.00147 0 0.06451 0.93549 0 0.03293 0.96707 0.01476 0.21295 0.77229 0 0.06503 0.93497 0.00002 0.12176 0.87822 0.01484 0.21339 0.77177 0 0.01715 0.98285 0 0.065 0.935 0.01481 0.21324 0.77195 0 0.06629 0.93371 0.00002 0.12177 0.87821 0 0.00868 0.99132 0 0.03367 0.96633 0 0.06356 0.93644 0 0.03366 0.96634 0 1 0 0 0.01719 0.98281 0.2158 0.7842 0 0 1 0 0 0.00117 0.99883 0.2158 0.7842 0 0 0.01718 0.98282 0.00002 0.12178 0.8782 0 0.03441 0.96559 0 0.00869 0.99131 0 0.00868 0.99132 0.12129 0.87871 0 0 0.00437 0.99563 0 0.00869 0.99131 0.00001 0.1218 0.87819 0 0.0649 0.9351 0.01484 0.21342 0.77173 0.01481 0.21324 0.77195 0 0.06503 0.93497 0 0.90723 0.09277 0 0.01718 0.98282 0 0.00886 0.99114 0 0.00202 0.99798 0 0.06467 0.93533 0.00001 0.12174 0.87825 0.00004 0.12117 0.87879 0.01471 0.21265 0.77263 0 1 0 0 0.03164 0.96836 0 1 0 0 0.01719 0.98281
-20:92865 T C 0.99719 0.00281 0 0.99423 0.00577 0 0.98812 0.01188 0 0.94399 0.05517 0.00084 0.99859 0.00141 0 0.97443 0.02557 0 0.99911 0.00089 0 0.99686 0.00314 0 0.99824 0.00176 0 0.9854 0.0146 0 0.99357 0.00643 0 0.99286 0.00714 0 0.97488 0.02512 0 0.99425 0.00575 0 0.98538 0.01462 0 0.99683 0.00317 0 0.98724 0.01276 0 0.97819 0.02181 0 0.9996 0.0004 0 0.99478 0.00522 0 0.99859 0.00141 0 0.9996 0.0004 0 0.99836 0.00164 0 0.99923 0.00077 0 0.99637 0.00363 0 0.99836 0.00164 0 0.9782 0.0218 0 0.99812 0.00188 0 0.99237 0.00763 0 0.99716 0.00284 0 0.99354 0.00646 0 0.99353 0.00647 0 0.99842 0.00158 0 0.98517 0.01483 0 0.99961 0.00039 0 0.99269 0.00731 0 0.99956 0.00044 0 0.99958 0.00042 0 0.99637 0.00363 0 0.99241 0.00759 0 0 1 0 0.94862 0.0507 0.00068 0.99643 0.00357 0 0.94894 0.05039 0.00067 0.95144 0.04803 0.00052 0.9993 0.0007 0 0 1 0 0.99414 0.00586 0 0.99726 0.00274 0
-20:92891 A G 0.99951 0.00049 0 0.99953 0.00047 0 0.99801 0.00199 0 0.99215 0.0078 0.00005 0.99635 0.00365 0 0.99636 0.00364 0 0.9963 0.0037 0 0.99631 0.00369 0 0.9932 0.0068 0 0.99955 0.00045 0 0.99816 0.00184 0 0.99988 0.00012 0 0.99772 0.00228 0 0.99623 0.00377 0 0.99994 0.00006 0 0.99994 0.00006 0 0.99909 0.00091 0 0.99909 0.00091 0 0.99977 0.00023 0 0.99955 0.00045 0 0.99802 0.00198 0 0.99998 0.00002 0 0.99994 0.00006 0 0.99994 0.00006 0 0.99977 0.00023 0 0.99994 0.00006 0 0.99978 0.00022 0 0.99977 0.00023 0 0.99955 0.00045 0 0.99989 0.00011 0 0.99817 0.00183 0 0.99999 0.00001 0 0.99999 0.00001 0 0.99639 0.00361 0 0.99999 0.00001 0 0.99908 0.00092 0 0.99989 0.00011 0 0.99989 0.00011 0 0.99994 0.00006 0 0.99994 0.00006 0 0 0.15512 0.84488 0.99236 0.00759 0.00005 0.99989 0.00011 0 0.98374 0.01621 0.00006 0.99628 0.00372 0 0.99633 0.00367 0 0.84719 0.15281 0 0.99998 0.00002 0 0.99989 0.00011 0
-20:93440 A G 0 1 0 0.74169 0.25831 0 0.55104 0.38203 0.06693 0.54996 0.38279 0.06725 0.85119 0.14881 0 0 0.59159 0.40841 0.01216 0.98755 0.0003 0.85119 0.14881 0 0.95888 0.04112 0 0.85119 0.14881 0 0.00065 0.74204 0.25732 0.85115 0.14885 0 0.74158 0.25842 0 0.99462 0.00538 0 0.91941 0.08059 0 0.00075 0.99925 0 0.74166 0.25834 0 0.91941 0.08059 0 0.91937 0.08063 0 0.74169 0.25831 0 0.5512 0.38192 0.06689 0.47351 0.43649 0.08999 0.92113 0.07887 0 0.71688 0.28312 0 0 0.99976 0.00024 0 0.56259 0.43741 0.55114 0.38195 0.06691 0 0.39333 0.60667 0 0.59151 0.40849 0.55114 0.38195 0.06691 0.55114 0.38195 0.06691 0.85119 0.14881 0 0.00244 0.99756 0 0.00116 0.99872 0.00012 0.91941 0.08059 0 0.74168 0.25832 0 0.85115 0.14885 0 0.85119 0.14881 0 0.00142 0.72682 0.27177 0.00625 0.99375 0 0.98426 0.01574 0 0.55012 0.38268 0.06721 0 1 0 0.00056 0.72704 0.2724 0.68983 0.31013 0.00004 0.98908 0.01092 0 0.96533 0.03467 0 0.85119 0.14881 0 0.91941 0.08059 0
-20:93499 T C 0.99693 0.00307 0 0.99321 0.00675 0.00004 0.99601 0.00399 0 0.99641 0.00359 0 0.99822 0.00178 0 0.9965 0.0035 0 0.99888 0.00112 0 0.99987 0.00013 0 0.98944 0.01055 0 0.99919 0.00081 0 0.99926 0.00074 0 0.9964 0.0036 0 0.99159 0.00837 0.00004 0.99635 0.00365 0 0.99364 0.00633 0.00004 0.99918 0.00082 0 0.99979 0.00021 0 0.99958 0.00042 0 0.99956 0.00044 0 0.99913 0.00087 0 0.99769 0.00231 0 0.99608 0.00392 0 0.99906 0.00094 0 0.99833 0.00167 0 0.99828 0.00172 0 0.99676 0.00324 0 0.99959 0.00041 0 0.99912 0.00088 0 0.99831 0.00169 0 0.99838 0.00162 0 0.99913 0.00087 0 0.9933 0.00667 0.00004 0.9999 0.0001 0 0.99913 0.00087 0 0.9996 0.0004 0 0.99956 0.00044 0 0.99917 0.00083 0 0.99835 0.00165 0 0.9996 0.0004 0 0.99979 0.00021 0 0 0.00477 0.99523 0.99576 0.00424 0 0.99974 0.00026 0 0.96382 0.036 0.00018 0.99639 0.00361 0 0.99345 0.00651 0.00004 0 1 0 0.99287 0.00709 0.00004 0.99921 0.00079 0
-20:93863 G A 0.99486 0.00514 0 0.97953 0.02047 0 0.9781 0.0219 0 0.98961 0.01039 0 0.99489 0.00511 0 0.97953 0.02047 0 0.99865 0.00135 0 0.96001 0.03999 0 0.96015 0.03985 0 0.99743 0.00257 0 0.97952 0.02048 0 0.96001 0.03999 0 0.92192 0.07641 0.00167 0.99489 0.00511 0 0.92187 0.07646 0.00167 0.95468 0.04532 0 0.97952 0.02048 0 0.98939 0.01061 0 0.96 0.04 0 0.96001 0.03999 0 0.9894 0.0106 0 0.99393 0.00607 0 0.97953 0.02047 0 0.99444 0.00556 0 0.96001 0.03999 0 0.06479 0.89518 0.04004 0.96001 0.03999 0 0.97571 0.02429 0 0.99489 0.00511 0 0.96001 0.03999 0 0.98963 0.01037 0 0.96002 0.03998 0 0.91016 0.08786 0.00198 0.92187 0.07646 0.00167 0.97952 0.02048 0 0.98963 0.01037 0 0.96 0.04 0 0.96001 0.03999 0 0.95551 0.04448 0 0.98739 0.01261 0 0.99999 0.00001 0 0.92171 0.07661 0.00167 0.9527 0.0473 0 0.95524 0.04476 0 0.91256 0.08552 0.00191 0.96001 0.03999 0 0.98965 0.01035 0 0.96003 0.03997 0 0 0.99934 0.00066
-20:93931 G A 0 0.99985 0.00015 0.93638 0.06361 0 0.93472 0.06527 0.00001 0.0192 0.98078 0.00003 0.9359 0.0641 0.00001 0.93604 0.06396 0 0.9667 0.0333 0 0.99156 0.00844 0 0.93422 0.06576 0.00002 0.99176 0.00824 0 0.00679 0.99171 0.0015 0.87582 0.12003 0.00415 0.8734 0.12229 0.00431 0.93549 0.0645 0.00001 0.98326 0.01674 0 0.37171 0.62827 0.00002 0.96682 0.03318 0 0.98368 0.01632 0 0.87636 0.11954 0.0041 0.99784 0.00216 0 0.93637 0.06363 0 0 0.79207 0.20793 0.9831 0.0169 0 0.5847 0.4153 0 0.93493 0.06501 0.00006 0.00493 0.99507 0 0.96658 0.03342 0 0 1 0 0.93445 0.06554 0 0.98369 0.01631 0 0.93662 0.06338 0 0.93496 0.06502 0.00002 0.22053 0.73094 0.04853 0.96677 0.03323 0 0.99173 0.00827 0 0.96688 0.03312 0 0.96655 0.03345 0 0.98317 0.01683 0 0.51234 0.48763 0.00003 0 1 0 0.99989 0.00011 0 0.92332 0.07667 0.00001 0 0.79125 0.20875 0.44399 0.52273 0.03329 0.25047 0.70273 0.0468 0.96622 0.03378 0 0.98318 0.01682 0 0.93572 0.06428 0 0.99145 0.00855 0
-20:94091 T C 0.99723 0.00277 0 0.99915 0.00085 0 0.99896 0.00104 0 0.99482 0.00518 0 0.99958 0.00042 0 0.99913 0.00087 0 0.99826 0.00174 0 0.99751 0.00249 0 0.98952 0.01047 0.00002 0.99985 0.00015 0 0.99966 0.00034 0 0.99818 0.00182 0 0.99686 0.00314 0 0.99829 0.00171 0 0.99992 0.00008 0 0.99919 0.00081 0 0.99865 0.00135 0 0.99936 0.00064 0 0.99956 0.00044 0 0.99931 0.00069 0 0.99784 0.00216 0 0.99844 0.00156 0 0.99734 0.00266 0 0.99319 0.00681 0 0.99851 0.00149 0 0.99859 0.00141 0 0.99984 0.00016 0 0.98916 0.01084 0 0.99925 0.00075 0 0.99992 0.00008 0 0.99924 0.00076 0 0.99956 0.00044 0 0.97599 0.02394 0.00007 0.99928 0.00072 0 0.99992 0.00008 0 0.99927 0.00073 0 0.99983 0.00017 0 0.99981 0.00019 0 0.99889 0.00111 0 0.99863 0.00137 0 0 0.00014 0.99986 0.99742 0.00258 0 0.97708 0.02281 0.00011 0.9596 0.0404 0 0.99833 0.00167 0 0.99965 0.00035 0 0 1 0 0.99803 0.00197 0 0.99969 0.00031 0
-20:94528 T G 0.99838 0.00162 0 0.99898 0.00102 0 0.99581 0.00418 0.00001 0.99843 0.00157 0 0.99905 0.00095 0 0.99809 0.00191 0 0.99605 0.00394 0.00001 0.99902 0.00098 0 0.98896 0.01102 0.00002 0.9991 0.0009 0 0.99851 0.00149 0 0.99971 0.00029 0 0.99689 0.00311 0 0.99887 0.00113 0 0.9991 0.0009 0 0.99706 0.00294 0 0.9982 0.0018 0 0.99909 0.00091 0 0.99978 0.00022 0 0.99812 0.00188 0 0.99578 0.00422 0.00001 0.99937 0.00063 0 0.99804 0.00196 0 0.9989 0.0011 0 0.99952 0.00048 0 0.99861 0.00139 0 0.99955 0.00045 0 0.99927 0.00073 0 0.99823 0.00177 0 0.9991 0.0009 0 0.99909 0.00091 0 0.99949 0.00051 0 0.99567 0.00433 0 0.99817 0.00183 0 0.99989 0.00011 0 0.99815 0.00185 0 0.99911 0.00089 0 0.99818 0.00182 0 0.9972 0.0028 0 0.99967 0.00033 0 0 0.00015 0.99985 0.99728 0.00272 0 0.99875 0.00125 0 0.96404 0.03596 0 0.99787 0.00213 0 0.99977 0.00023 0 0 0.99999 0.00001 0.9986 0.0014 0 0.99954 0.00046 0
-20:94592 T A 0.99008 0.00992 0 0.99933 0.00067 0 0.99715 0.00285 0 0.9987 0.0013 0 0.99886 0.00114 0 0.99932 0.00068 0 0.99863 0.00137 0 0.99907 0.00093 0 0.99027 0.00972 0.00001 0.99995 0.00005 0 0.99033 0.00967 0 0.99858 0.00142 0 0.99731 0.00269 0 0.99921 0.00079 0 0.99988 0.00012 0 0.99847 0.00153 0 0.99974 0.00026 0 0.99952 0.00048 0 0.99932 0.00068 0 0.99908 0.00092 0 0.99822 0.00178 0 0.98855 0.01145 0 0.99938 0.00062 0 0.99339 0.00661 0 0.99942 0.00058 0 0.99727 0.00273 0 0.99976 0.00024 0 0.98941 0.01059 0 0.99998 0.00002 0 0.99978 0.00022 0 0.99943 0.00057 0 0.99885 0.00115 0 0.98774 0.01226 0 0.99947 0.00053 0 0.99915 0.00085 0 0.99898 0.00102 0 0.99988 0.00012 0 0.99908 0.00092 0 0.99993 0.00007 0 0.99461 0.00539 0 0 0.83629 0.16371 0.99873 0.00127 0 0.99415 0.00585 0 0.98655 0.01345 0 0.98811 0.01189 0 0.99974 0.00026 0 0.93217 0.06763 0.00019 0.99841 0.00159 0 0.99915 0.00085 0
-20:94952 G T 0.97583 0.02417 0 0.99967 0.00033 0 0.99493 0.00507 0 0.95939 0.04048 0.00013 0.9945 0.0055 0 0.9969 0.0031 0 0.99688 0.00312 0 0.99497 0.00503 0 0.98798 0.01195 0.00007 0.99876 0.00124 0 0.96878 0.03111 0.00011 0.99597 0.00403 0 0.99271 0.00729 0 0.99405 0.00595 0 0.99936 0.00064 0 0 0.99999 0.00001 0.99477 0.00523 0 0.99939 0.00061 0 0.99543 0.00457 0 0.99008 0.00986 0.00007 0.99927 0.00073 0 0 1 0 0.99746 0.00254 0 0.0002 0.9998 0 0.99859 0.00141 0 0.00001 0.9896 0.01039 0.9898 0.01013 0.00007 0.01936 0.97546 0.00519 0.98752 0.01241 0.00007 0.9993 0.0007 0 0.99927 0.00073 0 0.98912 0.01082 0.00007 0 1 0 0.99464 0.00536 0 0.99877 0.00123 0 0.99814 0.00186 0 0.99577 0.00423 0 0.99736 0.00264 0 0.30783 0.69217 0 0 0.99957 0.00043 0.98905 0.01095 0 0.96778 0.03206 0.00017 0 0.99986 0.00014 0.35864 0.64135 0.00001 0.0004 0.9996 0 0.9895 0.01044 0.00007 0.99872 0.00128 0 0.99697 0.00303 0 0.99515 0.00485 0
-20:95052 T C 0.99758 0.00242 0 0.99525 0.00475 0 0.99486 0.00514 0 0.99534 0.00466 0 0.99768 0.00232 0 0.99759 0.00241 0 0.99756 0.00244 0 0.9976 0.0024 0 0.99513 0.00487 0 0.99526 0.00474 0 0.99539 0.00461 0 0.99756 0.00244 0 0.99489 0.00511 0 0.9976 0.0024 0 0.99941 0.00059 0 0.99939 0.00061 0 0.99761 0.00239 0 0.99762 0.00238 0 0.99752 0.00248 0 0.99053 0.00942 0.00005 0.99525 0.00475 0 0.99879 0.00121 0 0.9997 0.0003 0 0.99875 0.00125 0 0.99061 0.00934 0.00005 0.9994 0.0006 0 0.99881 0.00119 0 0.99051 0.00948 0.00001 0.9976 0.0024 0 0.9994 0.0006 0 0.99525 0.00475 0 0.99529 0.00471 0 0.99939 0.00061 0 0.99761 0.00239 0 0.99971 0.00029 0 0.99018 0.00977 0.00005 0.99936 0.00064 0 0.99879 0.00121 0 0.96423 0.03577 0 0.99941 0.00059 0 0 1 0 0.99437 0.00563 0 0.99938 0.00062 0 0.91404 0.08561 0.00035 0.99885 0.00115 0 0.99059 0.00936 0.00005 0 0.96513 0.03487 0.99522 0.00478 0 0.99941 0.00059 0
-20:95093 T G 0.99934 0.00066 0 0.9994 0.0006 0 0.99982 0.00018 0 0.99872 0.00128 0 0.99992 0.00008 0 0.99935 0.00065 0 0.99938 0.00062 0 0.99985 0.00015 0 0.99966 0.00034 0 0.9994 0.0006 0 0.99951 0.00049 0 0.99968 0.00032 0 0.99821 0.00179 0 0.99996 0.00004 0 0.99985 0.00015 0 0.94865 0.05132 0.00003 0.99969 0.00031 0 0.9997 0.0003 0 0.99869 0.00131 0 0.99992 0.00008 0 0.99998 0.00002 0 0.99655 0.00345 0 0.9994 0.0006 0 0.99316 0.00684 0 0.9997 0.0003 0 0.99831 0.00169 0 0.99938 0.00062 0 0.94852 0.05145 0.00003 0.99966 0.00034 0 0.99998 0.00002 0 0.9994 0.0006 0 0.99992 0.00008 0 0.94852 0.05145 0.00003 0.99968 0.00032 0 1 0 0 0.99998 0.00002 0 0.99908 0.00092 0 0.9994 0.0006 0 0.98702 0.01298 0 0.99831 0.00169 0 0 0.50444 0.49556 0.99761 0.00239 0 0.94852 0.05145 0.00003 0.9318 0.0682 0 0.99312 0.00688 0 0.99984 0.00016 0 0.58486 0.41514 0 0.99878 0.00122 0 0.9997 0.0003 0
-20:96166 C T 0.99983 0.00017 0 1 0 0 0.99998 0.00002 0 0.99994 0.00006 0 1 0 0 0.99994 0.00006 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.99957 0.00043 0 1 0 0 0.99999 0.00001 0 1 0 0 0.99999 0.00001 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 0.99999 0.00001 0 1 0 0 1 0 0 1 0 0 1 0 0 0.99999 0.00001 0 0.99999 0.00001 0 1 0 0 1 0 0 0.99997 0.00003 0 1 0 0 0.99989 0.00011 0 0.99956 0.00044 0 1 0 0 1 0 0 1 0 0 0 0.36151 0.63849 0.99798 0.00202 0 1 0 0 0.90505 0.09495 0 1 0 0 0.99998 0.00002 0 0 1 0 1 0 0 1 0 0
-20:96298 T C 0.99824 0.00176 0 0 1 0 0.99911 0.00089 0 0.99651 0.00349 0 0.99978 0.00022 0 0.99911 0.00089 0 0.99638 0.00362 0 0.99911 0.00089 0 0.99989 0.00011 0 0.99818 0.00182 0 0.9982 0.0018 0 0.99638 0.00362 0 0.97183 0.02797 0.00021 0.99638 0.00362 0 0.99818 0.00182 0 0.99637 0.00363 0 0.99822 0.00178 0 0.99978 0.00022 0 0.99909 0.00091 0 0.99822 0.00178 0 0.99989 0.00011 0 0.99999 0.00001 0 0.99911 0.00089 0 0.99955 0.00045 0 0.99978 0.00022 0 0.99911 0.00089 0 0.99911 0.00089 0 0.99281 0.00719 0 0.99822 0.00178 0 0.99279 0.00721 0 0.98573 0.01427 0 0.9928 0.0072 0 0.99911 0.00089 0 0.99907 0.00093 0 0.99953 0.00047 0 0.99955 0.00045 0 0.9928 0.0072 0 0.99999 0.00001 0 0.99994 0.00006 0 0.99994 0.00006 0 0.99872 0.00128 0 0.9929 0.0071 0 0.98576 0.01424 0 0.99795 0.00205 0 0.99285 0.00715 0 0.99909 0.00091 0 0.99823 0.00177 0 1 0 0 0.99818 0.00182 0
-20:96931 A G 0.97873 0.02127 0 0.99804 0.00196 0 0.98969 0.01026 0.00005 0.98765 0.01235 0 0.9999 0.0001 0 0.99861 0.00139 0 0.99748 0.00252 0 0.99931 0.00069 0 0.99811 0.00189 0 0.99973 0.00027 0 0.99863 0.00137 0 0.9971 0.0029 0 0.99333 0.00667 0 0.99854 0.00146 0 0.99974 0.00026 0 0.00435 0.99565 0 0.99962 0.00038 0 0.99997 0.00003 0 0.99469 0.00531 0 0.99843 0.00157 0 0.99946 0.00054 0 0 1 0 0.99972 0.00028 0 0 1 0 0.99984 0.00016 0 0 1 0 0.9999 0.0001 0 0.00006 0.99994 0 0.99734 0.00266 0 0.99804 0.00196 0 0.99947 0.00053 0 0.99987 0.00013 0 0.00001 0.99999 0 0.99921 0.00079 0 0.99994 0.00006 0 0.99638 0.00362 0 0.99028 0.00967 0.00005 0.99888 0.00112 0 0 1 0 0 1 0 0 0.34069 0.65931 0.97012 0.02988 0 0 1 0 0.03083 0.95756 0.01161 0.00077 0.98972 0.00952 0.99906 0.00094 0 0 1 0 0.99875 0.00125 0 0.99993 0.00007 0
-20:97122 C T 0.99639 0.00361 0 1 0 0 0.99975 0.00025 0 0.99854 0.00146 0 0.99997 0.00003 0 0.99993 0.00007 0 0.9998 0.0002 0 0.99978 0.00022 0 0.99999 0.00001 0 1 0 0 0.99842 0.00158 0 0.99968 0.00032 0 0.99288 0.00711 0.00001 0.99991 0.00009 0 0.99996 0.00004 0 0 1 0 0.99994 0.00006 0 0.99999 0.00001 0 0.99992 0.00008 0 0.99989 0.00011 0 0.99998 0.00002 0 0 0.99999 0.00001 0.99997 0.00003 0 0 0.99995 0.00005 0.99993 0.00007 0 0.00051 0.99949 0 1 0 0 0 1 0 0.99952 0.00048 0 1 0 0 0.99997 0.00003 0 0.99996 0.00004 0 0.00003 0.99997 0 0.99989 0.00011 0 0.99998 0.00002 0 0.99843 0.00157 0 0.9995 0.0005 0 0.99997 0.00003 0 0.0663 0.9337 0 0 1 0 0.9999 0.0001 0 0.98176 0.01824 0 0.11439 0.88561 0 0.42811 0.57154 0.00035 0.03446 0.95909 0.00645 0.99985 0.00015 0 0.99989 0.00011 0 1 0 0 1 0 0
-20:97227 A C 0.98645 0.01355 0 0.99827 0.00173 0 0.99655 0.00345 0 0.99315 0.00685 0 0.99911 0.00089 0 0.99831 0.00169 0 0.99911 0.00089 0 0.98641 0.01359 0 0.99314 0.00686 0 0.99957 0.00043 0 0.98643 0.01357 0 0.99819 0.00181 0 0.98647 0.01353 0 0.99314 0.00686 0 0.98641 0.01359 0 0.99316 0.00684 0 0.99655 0.00345 0 0.99655 0.00345 0 0.99655 0.00345 0 0 0.99995 0.00005 0.99314 0.00686 0 0.99979 0.00021 0 0.99827 0.00173 0 0.99979 0.00021 0 0.98641 0.01359 0 0.99656 0.00344 0 0.99314 0.00686 0 0.99979 0.00021 0 0.99655 0.00345 0 0.99655 0.00345 0 0.99827 0.00173 0 0.99655 0.00345 0 0.99284 0.00716 0 0.97308 0.02673 0.00019 0.98641 0.01359 0 0.99655 0.00345 0 0.99314 0.00686 0 0.99314 0.00686 0 0.99298 0.00702 0 0.99827 0.00173 0 0.99992 0.00008 0 0.99322 0.00678 0 0.98643 0.01357 0 0.99557 0.00443 0 0.99658 0.00342 0 0.99314 0.00686 0 0.99956 0.00044 0 0.99827 0.00173 0 0.99831 0.00169 0
-20:97394 A G 0.99536 0.00464 0 0.99992 0.00008 0 0.99959 0.00041 0 0.99802 0.00198 0 0.99953 0.00047 0 0.99984 0.00016 0 0.99996 0.00004 0 0.9999 0.0001 0 0.99998 0.00002 0 0.99989 0.00011 0 0.99803 0.00197 0 0.99991 0.00009 0 0.99312 0.00688 0 0.99999 0.00001 0 0.99991 0.00009 0 0 1 0 0.99902 0.00098 0 0.99996 0.00004 0 0.99997 0.00003 0 0.99995 0.00005 0 0.99998 0.00002 0 0 1 0 1 0 0 0.54298 0.45702 0 0.99972 0.00028 0 0.00154 0.99846 0 0.99998 0.00002 0 0 1 0 0.99972 0.00028 0 0.99999 0.00001 0 0.99995 0.00005 0 0.99988 0.00012 0 0.54301 0.45699 0 0.99963 0.00037 0 0.99998 0.00002 0 0.99642 0.00358 0 0.99916 0.00084 0 0.99986 0.00014 0 0.54143 0.45857 0 0.37513 0.62487 0 0 0.36133 0.63867 0.97796 0.022 0.00004 0 0.99999 0.00001 0.42779 0.56873 0.00348 0 0.9999 0.0001 0.99979 0.00021 0 0 0.99999 0.00001 0.99994 0.00006 0 1 0 0
-20:97395 G A 0.99965 0.00035 0 0.99997 0.00003 0 0.99996 0.00004 0 0.99988 0.00012 0 1 0 0 0.99988 0.00012 0 1 0 0 1 0 0 1 0 0 1 0 0 0.99985 0.00015 0 1 0 0 0.99923 0.00077 0 1 0 0 0.99994 0.00006 0 1 0 0 0.99997 0.00003 0 0.99999 0.00001 0 0.99999 0.00001 0 1 0 0 1 0 0 1 0 0 1 0 0 0.99995 0.00005 0 0.99997 0.00003 0 0.99999 0.00001 0 1 0 0 1 0 0 0.99999 0.00001 0 0.99999 0.00001 0 0.99997 0.00003 0 1 0 0 1 0 0 0.99991 0.00009 0 1 0 0 0.99928 0.00072 0 0.99944 0.00056 0 0.99999 0.00001 0 1 0 0 0.99999 0.00001 0 0 0.36147 0.63853 0.9971 0.0029 0 1 0 0 0.87979 0.11993 0.00029 0.99994 0.00006 0 0.99996 0.00004 0 0 1 0 1 0 0 1 0 0
-20:98930 G A 0.99359 0.00641 0 0.99994 0.00006 0 0.99921 0.00079 0 0.99724 0.00276 0 0.9995 0.0005 0 0.99993 0.00007 0 0.99971 0.00029 0 0.99971 0.00029 0 0.99993 0.00007 0 0.99986 0.00014 0 0.99759 0.00241 0 0.99962 0.00038 0 0.99116 0.00883 0.00001 0.9999 0.0001 0 0.99997 0.00003 0 0 1 0 0.99901 0.00099 0 0.99997 0.00003 0 0.9999 0.0001 0 0.99985 0.00015 0 0.99996 0.00004 0 0 0.99995 0.00005 0.99996 0.00004 0 0 1 0 0.99971 0.00029 0 0 1 0 0.99998 0.00002 0 0 0.99997 0.00003 0.99935 0.00065 0 1 0 0 0.99998 0.00002 0 0.99983 0.00017 0 0 1 0 0.99969 0.00031 0 0.99997 0.00003 0 0.99678 0.00322 0 0.99944 0.00056 0 0.99985 0.00015 0 0 0.99999 0.00001 0 1 0 0.99986 0.00014 0 0.97606 0.02389 0.00004 0 0.99873 0.00127 0.40728 0.59272 0 0 0.9916 0.0084 0.99974 0.00026 0 0.99987 0.00013 0 0.99992 0.00008 0 1 0 0
-20:99667 C T 0.98466 0.01534 0 0.99225 0.00775 0 0.98466 0.01534 0 0.99225 0.00775 0 0.99225 0.00775 0 0.98466 0.01534 0 0.99804 0.00196 0 0.98466 0.01534 0 0.98466 0.01534 0 0.98465 0.01534 0 0.99225 0.00775 0 0.99225 0.00775 0 0.96962 0.03014 0.00024 0.96962 0.03014 0.00024 0.99225 0.00775 0 0.99804 0.00196 0 0.98466 0.01534 0 0.99809 0.00191 0 0.9961 0.0039 0 0.98466 0.01534 0 0.96962 0.03014 0.00024 0.98466 0.01534 0 0.99225 0.00775 0 0.99225 0.00775 0 0.9961 0.0039 0 0 0.99834 0.00166 0.99809 0.00191 0 0.99225 0.00775 0 0.99225 0.00775 0 0.999 0.001 0 0.99225 0.00775 0 0.98466 0.01534 0 0.99809 0.00191 0 0.98466 0.01534 0 0.96962 0.03014 0.00024 0.98466 0.01534 0 0.98466 0.01534 0 0.96962 0.03014 0.00024 0.99225 0.00775 0 0.96962 0.03014 0.00024 0.99902 0.00098 0 0.96962 0.03014 0.00024 0.98466 0.01534 0 0.96962 0.03014 0.00024 0.9961 0.0039 0 0.98466 0.01534 0 0.98466 0.01534 0 0.98466 0.01534 0 0.9961 0.0039 0
-20:99801 G A 0.99199 0.00801 0 0.99597 0.00403 0 0.96863 0.03111 0.00026 0.96863 0.03111 0.00026 0.99199 0.00801 0 0.96863 0.03111 0.00026 0.98415 0.01585 0 0.99199 0.00801 0 0.98415 0.01585 0 0.99901 0.00099 0 0.99901 0.00099 0 0.99597 0.00403 0 0.98415 0.01585 0 0.98415 0.01585 0 0.99797 0.00203 0 0.98415 0.01585 0 0.98415 0.01585 0 0.99987 0.00013 0 0.99901 0.00099 0 0.99597 0.00403 0 0.99597 0.00403 0 0.96863 0.03111 0.00026 0.98415 0.01585 0 0.99802 0.00198 0 0.98415 0.01585 0 0.99802 0.00198 0 0.99901 0.00099 0 0.99199 0.00801 0 0.99597 0.00403 0 0.99597 0.00403 0 0.99802 0.00198 0 0.99797 0.00203 0 0.99199 0.00801 0 0.99199 0.00801 0 0.99597 0.00403 0 0.96863 0.03111 0.00026 0.99199 0.00801 0 0.98415 0.01585 0 0.99199 0.00801 0 0.9995 0.0005 0 0 0.94139 0.05861 0.96863 0.03111 0.00026 0.99199 0.00801 0 0.96863 0.03111 0.00026 0.99597 0.00403 0 0.98415 0.01585 0 0.99199 0.00801 0 0.99802 0.00198 0 0.99802 0.00198 0

public/testdata/Beagle/inttestbgl.input.vcf

@@ -1,247 +0,0 @@
-##fileformat=VCFv3.3
-##FILTER=FDRtranche12.50to25.00,"FDR tranche level at qual 1.8"
-##FILTER=FDRtranche25.00to35.00+,"FDR tranche level at qual > 4.8"
-##FILTER=FDRtranche5.00to12.50,"FDR tranche level at qual 4.8"
-##FILTER=HARD_TO_VALIDATE,"(MQ0 / (1.0 * DP)) > 0.1"
-##FILTER=InDel,"Overlaps a user-input mask"
-##FILTER=SnpCluster,"SNPs found in clusters"
-##FORMAT=DP,1,Integer,"Read Depth (only filtered reads used for calling)"
-##FORMAT=GL,3,Float,"Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic"
-##FORMAT=GQ,1,Float,"Genotype Quality"
-##FORMAT=GT,1,String,"Genotype"
-##INFO=AB,1,Float,"Allele Balance for hets (ref/(ref+alt))"
-##INFO=AC,1,Integer,"Allele count in genotypes, for each ALT allele, in the same order as listed"
-##INFO=AF,1,Float,"Allele Frequency"
-##INFO=AN,1,Integer,"Total number of alleles in called genotypes"
-##INFO=DB,1,Integer,"dbSNP Membership"
-##INFO=DP,1,Integer,"Total Depth"
-##INFO=Dels,1,Float,"Fraction of Reads Containing Spanning Deletions"
-##INFO=HRun,1,Integer,"Largest Contiguous Homopolymer Run of Variant Allele In Either Direction"
-##INFO=HaplotypeScore,1,Float,"Consistency of the site with two (and only two) segregating haplotypes"
-##INFO=MQ,1,Float,"RMS Mapping Quality"
-##INFO=MQ0,1,Integer,"Total Mapping Quality Zero Reads"
-##INFO=OQ,1,Float,"The original variant quality score"
-##INFO=QD,1,Float,"Variant Confidence/Quality by Depth"
-##INFO=SB,1,Float,"Strand Bias"
-##UG_assume_single_sample_reads=null
-##UG_bam_file_used=CEUTSI.chr20.cleaned.bam
-##UG_base_model=EMPIRICAL
-##UG_cap_base_quality_by_mapping_quality=false
-##UG_genotype=false
-##UG_genotype_model=JOINT_ESTIMATE
-##UG_heterozygosity=0.0010
-##UG_max_deletion_fraction=0.05
-##UG_max_mismatches_in_40bp_window=3
-##UG_min_base_quality_score=10
-##UG_min_mapping_quality_score=10
-##UG_noSLOD=false
-##UG_output_all_callable_bases=false
-##UG_platform=null
-##UG_standard_min_confidence_threshold_for_calling=10.0
-##UG_standard_min_confidence_threshold_for_emitting=30.0
-##UG_trigger_min_confidence_threshold_for_calling=30.0
-##UG_trigger_min_confidence_threshold_for_emitting=30.0
-##UG_use_reads_with_bad_mates=false
-##reference=human_g1k_v37.fasta
-##source=UnifiedGenotyper
-##source=VariantOptimizer
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA07056	NA11892	NA11893	NA12347	NA12348	NA12383	NA12413	NA12546	NA12775	NA12777	NA12778	NA20502	NA20505	NA20508	NA20509	NA20510	NA20512	NA20515	NA20516	NA20517	NA20518	NA20519	NA20520	NA20522	NA20524	NA20525	NA20527	NA20528	NA20529	NA20530	NA20531	NA20534	NA20535	NA20538	NA20539	NA20540	NA20541	NA20542	NA20543	NA20544	NA20582	NA20586	NA20588	NA20589	NA20752	NA20753	NA20754	NA20755	NA20756	
-20	60251	.	T	C	6.78	0	AB=0.50;AC=1;AF=0.01;AN=98;DB=0;DP=181;Dels=0.00;HRun=0;HaplotypeScore=21.57;MQ=58.05;MQ0=0;OQ=15.98;QD=4.00;SB=-503.94	GT:DP:GL:GQ	0/0:3:-0.00,-0.90,-12.19:9.03	0/0:2:-0.01,-0.61,-6.42:6.00	0/0:2:-0.00,-0.60,-7.73:6.02	0/0:4:-0.00,-1.21,-15.02:12.04	0/0:5:-0.03,-1.53,-15.30:14.99	0/0:3:-0.00,-0.90,-11.28:9.03	0/0:3:-0.00,-0.91,-11.18:9.03	0/0:9:-0.03,-2.73,-31.82:27.03	0/1:4:-6.37,-1.21,-7.04:51.60	0/0:10:-0.03,-3.03,-32.50:30.05	0/0:3:-0.00,-0.90,-11.18:9.03	0/0:4:-0.00,-1.21,-13.85:12.03	0/0:1:-0.01,-0.31,-2.57:3.00	0/0:2:-0.00,-0.60,-8.02:6.02	0/0:4:-0.00,-1.21,-14.03:12.03	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.72:6.02	0/0:2:-0.00,-0.60,-7.72:6.02	0/0:2:-0.00,-0.60,-7.43:6.02	0/0:6:-0.01,-1.81,-21.03:18.05	0/0:4:-0.00,-1.21,-14.66:12.04	0/0:2:-0.00,-0.60,-7.53:6.02	0/0:4:-0.00,-1.21,-14.56:12.04	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-10.68:9.03	0/0:4:-0.02,-1.22,-12.96:12.00	0/0:6:-0.01,-1.82,-20.37:18.04	0/0:2:-0.00,-0.60,-6.41:6.01	0/0:8:-0.00,-2.41,-30.11:24.08	0/0:6:-0.00,-1.81,-21.77:18.05	0/0:2:-0.00,-0.60,-7.72:6.02	0/0:3:-0.00,-0.90,-11.89:9.03	0/0:4:-0.01,-1.21,-13.73:12.03	0/0:2:-0.00,-0.60,-7.92:6.02	0/0:6:-0.00,-1.81,-21.98:18.05	0/0:3:-0.00,-0.90,-11.38:9.03	0/0:1:-0.00,-0.30,-3.56:3.01	0/0:2:-0.00,-0.60,-7.72:6.02	0/0:2:-0.00,-0.60,-7.51:6.02	0/0:6:-0.01,-1.81,-21.17:18.05	0/0:5:-0.00,-1.51,-18.60:15.05	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.52:6.02	0/0:3:-0.00,-0.90,-11.29:9.03	0/0:3:-0.00,-0.90,-11.18:9.03	0/0:4:-0.00,-1.21,-14.82:12.04	0/0:7:-0.01,-2.11,-24.32:21.06	0/0:6:-0.00,-1.81,-21.47:18.05
-20	60321	.	G	T	1.42	FDRtranche25.00to35.00	AB=0.33;AC=1;AF=0.01;AN=98;DB=0;DP=187;Dels=0.00;HRun=2;HaplotypeScore=22.93;MQ=56.25;MQ0=0;OQ=15.86;QD=5.29;SB=-504.38	GT:DP:GL:GQ	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:5:-0.00,-1.51,-16.32:15.03	0/0:2:-0.00,-0.60,-6.26:6.01	0/0:8:-0.03,-2.43,-24.79:23.96	0/0:5:-0.03,-1.52,-12.92:14.92	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:5:-0.02,-1.52,-14.73:14.99	0/0:5:-0.01,-1.51,-13.57:14.97	0/0:3:-0.00,-0.90,-9.16:9.02	0/0:8:-0.03,-2.43,-23.90:23.98	0/0:3:-0.00,-0.90,-9.42:9.02	0/0:3:-0.00,-0.90,-9.10:9.02	0/0:1:-0.04,-0.31,-1.30:2.78	0/0:2:-0.00,-0.60,-6.36:6.01	0/0:5:-0.00,-1.51,-16.29:15.04	0/1:3:-6.04,-0.91,-1.80:8.95	0/0:8:-0.00,-2.41,-26.37:24.06	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:2:-0.00,-0.60,-5.81:6.01	0/0:3:-0.00,-0.90,-10.02:9.02	./.:-1:0,0,0:-1	0/0:6:-0.01,-1.81,-18.59:18.04	0/0:6:-0.01,-1.81,-17.56:18.02	0/0:4:-0.01,-1.21,-11.97:12.02	0/0:4:-0.01,-1.21,-11.47:12.01	0/0:2:-0.00,-0.60,-6.21:6.01	0/0:7:-0.04,-2.12,-19.33:20.79	0/0:5:-0.01,-1.51,-14.57:14.97	./.:-1:0,0,0:-1	0/0:4:-0.02,-1.21,-9.82:11.94	0/0:2:-0.01,-0.61,-4.56:5.96	0/0:2:-0.00,-0.60,-6.16:6.01	0/0:3:-0.01,-0.91,-8.67:8.99	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.71:6.02	0/0:6:-0.01,-1.81,-17.83:18.02	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:3:-0.00,-0.90,-9.76:9.02	0/0:2:-0.00,-0.60,-5.36:6.00	0/0:6:-0.01,-1.81,-16.79:18.01	0/0:3:-0.03,-0.92,-7.07:8.92	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:1:-0.01,-0.31,-1.96:2.96	0/0:3:-0.00,-0.90,-9.72:9.02	0/0:1:-0.00,-0.30,-3.16:3.01	0/0:4:-0.00,-1.21,-12.16:12.02	./.:-1:0,0,0:-1	0/0:6:-0.01,-1.81,-18.53:18.02	0/0:8:-0.04,-2.42,-22.94:23.89
-20	60467	.	G	C	0.03	FDRtranche25.00to35.00+	AB=0.71;AC=3;AF=0.06;AN=98;DB=0;DP=162;Dels=0.01;HRun=1;HaplotypeScore=63.31;MQ=55.93;MQ0=0;OQ=46.69;QD=1.95;SB=-422.92	GT:DP:GL:GQ	0/0:2:-0.02,-0.62,-5.44:6.00	0/0:3:-0.02,-0.92,-11.03:9.00	0/0:3:-0.00,-0.90,-11.94:9.03	0/0:2:-0.00,-0.60,-8.78:6.02	0/0:2:-0.00,-0.60,-7.58:6.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.95:3.01	0/0:7:-0.02,-2.12,-25.16:21.06	0/1:4:-2.90,-1.22,-10.79:16.78	0/0:2:-0.00,-0.60,-7.44:6.02	0/0:3:-0.01,-0.91,-10.59:9.02	0/0:2:-0.00,-0.60,-8.68:6.02	0/0:1:-0.00,-0.30,-3.65:3.01	0/0:2:-0.00,-0.60,-7.99:6.02	0/0:6:-0.00,-1.81,-23.77:18.06	./.:-1:0,0,0:-1	0/1:5:-4.03,-1.54,-12.93:24.91	./.:-1:0,0,0:-1	0/0:2:-0.01,-0.61,-6.54:6.02	0/0:7:-0.01,-1.81,-22.62:18.05	0/0:2:-0.00,-0.60,-7.74:6.02	0/0:6:-0.01,-1.81,-23.56:18.06	0/0:6:-0.03,-1.83,-22.36:18.03	0/0:2:-0.00,-0.60,-7.98:6.02	0/0:1:0.00,0.00,0.00:0.00	0/0:2:-0.00,-0.60,-8.48:6.02	0/0:4:-0.00,-1.21,-16.08:12.04	0/0:1:-0.00,-0.30,-3.89:3.01	0/0:2:-0.00,-0.60,-7.88:6.02	0/0:3:-0.00,-0.91,-10.94:9.03	0/0:1:-0.00,-0.30,-4.39:3.01	0/0:3:-0.00,-0.90,-12.88:9.03	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.69:3.01	0/1:5:-2.70,-1.52,-16.59:11.71	0/0:2:-0.00,-0.60,-7.59:6.02	./.:-1:0,0,0:-1	0/0:2:-0.05,-0.64,-5.49:5.97	0/0:3:-0.02,-0.92,-10.28:9.02	0/0:4:-0.03,-1.23,-13.88:12.01	0/0:1:-0.00,-0.30,-3.99:3.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.65:3.01	./.:-1:0,0,0:-1	0/0:1:-0.02,-0.32,-2.59:3.00	0/0:2:-0.02,-0.62,-5.94:6.00	0/0:5:-0.00,-1.51,-19.93:15.05	0/0:7:-0.02,-2.12,-26.16:21.05	0/0:4:-0.05,-1.25,-12.38:11.99
-20	60469	.	A	C	0.05	FDRtranche25.00to35.00+	AB=0.54;AC=11;AF=0.12;AN=98;DB=0;DP=171;Dels=0.00;HRun=1;HaplotypeScore=58.97;MQ=55.98;MQ0=0;OQ=46.69;QD=1.14;SB=-408.11	GT:DP:GL:GQ	0/1:2:-2.41,-0.61,-1.94:13.35	0/0:4:-0.05,-1.24,-11.07:11.87	0/0:3:-0.00,-0.90,-10.78:9.03	0/0:2:-0.04,-0.62,-4.58:5.81	0/1:4:-2.02,-1.22,-7.78:8.00	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.49:3.01	0/0:7:-1.80,-2.11,-19.81:3.09	0/0:5:-1.41,-1.52,-10.54:1.07	0/1:3:-2.10,-0.91,-6.34:11.96	0/0:3:-0.01,-0.91,-9.03:9.01	0/0:5:-0.00,-1.51,-16.36:15.04	1/1:1:-1.60,-0.31,-0.02:2.90	0/0:1:-0.00,-0.30,-3.59:3.01	0/0:5:-0.00,-1.51,-17.66:15.04	./.:-1:0,0,0:-1	0/1:5:-1.60,-1.51,-13.34:0.90	0/0:1:-1.37,-1.59,-2.05:2.18	0/0:1:-0.00,-0.30,-3.39:3.01	0/0:6:-0.01,-1.81,-19.30:18.04	0/0:2:-0.00,-0.60,-6.93:6.02	0/0:7:-0.02,-2.12,-19.50:21.01	0/1:6:-2.11,-1.81,-14.76:2.97	0/0:2:-0.00,-0.60,-6.93:6.02	0/0:1:-0.05,-0.33,-1.49:2.86	0/1:3:-1.20,-0.92,-6.02:2.82	0/0:3:-0.00,-0.90,-10.33:9.03	0/0:1:-0.00,-0.30,-2.84:3.00	0/1:3:-1.30,-0.92,-6.51:3.85	0/0:3:-0.00,-0.90,-10.28:9.03	0/0:2:-0.00,-0.60,-6.43:6.02	0/0:2:-0.00,-0.60,-6.98:6.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.84:3.00	0/0:3:-0.00,-0.90,-9.02:9.01	0/0:1:-0.00,-0.30,-3.49:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.59:6.02	0/0:3:-0.03,-0.92,-7.02:8.84	0/0:3:-0.01,-0.91,-9.07:9.01	0/0:1:-0.00,-0.30,-3.24:3.01	./.:-1:0,0,0:-1	0/1:2:-2.70,-0.60,-3.30:20.98	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.84:3.00	0/1:5:-1.73,-1.52,-10.98:2.05	0/0:5:-0.00,-1.51,-16.76:15.04	0/0:7:-0.01,-2.11,-22.10:21.04	0/0:6:-1.41,-1.82,-15.99:4.14
-20	60864	.	G	C	20.43	0	AB=0.60;AC=1;AF=0.01;AN=98;DB=0;DP=200;Dels=0.00;HRun=0;HaplotypeScore=29.58;MQ=57.91;MQ0=0;OQ=25.61;QD=5.12;SB=-529.44	GT:DP:GL:GQ	0/0:5:-0.00,-1.51,-21.02:15.05	0/0:5:-0.00,-1.51,-20.93:15.05	0/0:4:-0.00,-1.21,-16.78:12.04	0/0:3:-0.00,-0.90,-12.59:9.03	0/0:6:-0.00,-1.81,-23.82:18.06	0/0:3:-0.00,-0.90,-12.49:9.03	0/0:2:-0.00,-0.60,-8.38:6.02	0/0:7:-0.05,-2.15,-26.86:21.04	0/0:4:-0.00,-1.21,-15.43:12.04	0/0:10:-0.02,-3.03,-39.69:30.09	0/0:3:-0.00,-0.91,-11.93:9.03	0/0:1:-0.00,-0.30,-4.29:3.01	./.:-1:0,0,0:-1	0/0:5:-0.00,-1.51,-20.53:15.05	0/0:2:-0.00,-0.60,-8.24:6.02	0/0:1:-0.00,-0.30,-4.19:3.01	0/0:4:-0.00,-1.21,-16.63:12.04	0/0:5:-0.01,-1.51,-17.93:15.04	0/0:1:-0.00,-0.30,-4.29:3.01	0/0:2:-0.00,-0.60,-7.94:6.02	0/0:5:-0.00,-1.51,-22.56:15.05	0/0:9:-0.01,-2.71,-35.06:27.09	0/0:8:-0.00,-2.41,-33.10:24.08	0/0:2:-0.00,-0.60,-7.94:6.02	0/0:2:-0.00,-0.60,-8.24:6.02	0/0:6:-0.01,-1.81,-22.97:18.06	0/0:3:-0.00,-0.90,-12.63:9.03	0/0:6:-0.03,-1.83,-20.97:18.03	0/1:5:-7.64,-1.51,-11.93:61.33	0/0:4:-0.00,-1.21,-17.12:12.04	0/0:7:-0.02,-2.13,-26.26:21.05	0/0:3:-0.00,-0.90,-11.79:9.03	0/0:3:-0.00,-0.91,-11.98:9.03	./.:-1:0,0,0:-1	0/0:8:-0.00,-2.41,-33.55:24.08	0/0:3:-0.00,-0.90,-12.63:9.03	0/0:1:-0.00,-0.30,-3.75:3.01	0/0:2:-0.00,-0.61,-6.79:6.02	0/0:5:-0.00,-1.51,-19.13:15.05	0/0:1:-0.00,-0.30,-3.55:3.01	0/0:1:-0.00,-0.30,-3.65:3.01	0/0:3:-0.01,-0.91,-11.19:9.03	0/0:5:-0.00,-1.51,-19.13:15.05	0/0:3:-0.00,-0.90,-12.83:9.03	0/0:2:-0.00,-0.60,-7.79:6.02	0/0:4:-0.00,-1.21,-15.58:12.04	0/0:4:-0.01,-1.21,-15.48:12.04	0/0:5:-0.00,-1.51,-20.43:15.05	0/0:5:-0.01,-1.52,-19.02:15.04
-20	60982	.	G	C	0.10	FDRtranche25.00to35.00+	AB=0.67;AC=2;AF=0.02;AN=98;DB=0;DP=180;Dels=0.00;HRun=1;HaplotypeScore=27.96;MQ=56.10;MQ0=0;OQ=12.72;QD=2.12;SB=-470.97	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-7.88:6.02	0/0:3:-0.01,-0.91,-10.93:9.03	0/0:3:-0.00,-0.90,-13.23:9.03	0/0:3:-0.00,-0.90,-12.93:9.03	0/0:4:-0.00,-1.21,-16.42:12.04	0/0:4:-0.00,-1.21,-17.67:12.04	0/0:4:-0.00,-1.21,-16.08:12.04	0/0:6:-0.00,-1.81,-24.41:18.06	0/0:3:-0.00,-0.91,-11.98:9.03	0/0:9:-0.02,-2.73,-34.14:27.08	0/0:5:-0.00,-1.51,-21.52:15.05	0/0:2:-0.00,-0.60,-8.38:6.02	0/0:1:-0.00,-0.30,-4.29:3.01	0/0:2:-0.00,-0.60,-9.28:6.02	0/0:2:-0.00,-0.60,-7.84:6.02	0/1:3:-2.69,-0.92,-9.00:17.73	0/0:6:-0.03,-1.83,-23.71:18.03	0/0:2:-0.00,-0.60,-7.74:6.02	0/0:2:-0.00,-0.60,-7.84:6.02	0/0:2:-0.01,-0.61,-6.59:6.01	0/0:3:-0.00,-0.91,-12.03:9.03	0/0:2:-0.00,-0.60,-8.68:6.02	0/0:6:-0.00,-1.81,-24.72:18.06	0/0:4:-0.01,-1.22,-14.32:12.03	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.79:6.02	0/0:3:-0.00,-0.91,-10.99:9.03	0/0:3:-0.05,-0.95,-10.13:8.98	0/0:1:-0.00,-0.30,-4.49:3.01	0/0:4:-0.00,-1.21,-16.67:12.04	0/0:5:-0.00,-1.51,-20.27:15.05	0/0:1:-0.00,-0.30,-4.59:3.01	0/0:3:-0.01,-0.91,-11.43:9.03	0/0:1:-0.00,-0.30,-4.69:3.01	0/0:4:-0.01,-1.21,-15.28:12.04	0/0:2:-0.01,-0.61,-6.09:6.01	0/0:1:-0.00,-0.30,-3.69:3.01	0/0:1:-0.00,-0.30,-4.39:3.01	0/0:2:-0.00,-0.61,-7.34:6.02	0/0:3:-0.00,-0.91,-11.98:9.03	0/0:3:-0.00,-0.91,-11.13:9.03	./.:-1:0,0,0:-1	0/0:5:-0.01,-1.52,-17.92:15.04	./.:-1:0,0,0:-1	0/0:2:-0.04,-0.63,-6.04:5.98	0/0:4:-0.01,-1.21,-15.42:12.04	0/1:2:-3.89,-0.60,-4.39:32.89	0/0:10:-0.01,-3.02,-41.48:30.10	0/0:9:-0.02,-2.72,-36.20:27.08
-20	60998	.	A	C	0.05	FDRtranche25.00to35.00+	AB=0.57;AC=5;AF=0.05;AN=98;DB=0;DP=214;Dels=0.00;HRun=1;HaplotypeScore=51.60;MQ=55.33;MQ0=0;OQ=40.48;QD=2.25;SB=-440.00	GT:DP:GL:GQ	0/0:2:-0.01,-0.60,-4.88:5.98	0/0:1:-0.00,-0.30,-3.54:3.01	0/0:1:-0.00,-0.30,-3.44:3.01	0/0:1:-0.02,-0.31,-1.89:2.95	0/0:4:-0.05,-1.23,-8.81:11.83	0/0:3:-0.00,-0.90,-9.82:9.02	0/0:3:-0.01,-0.91,-7.92:8.98	0/0:7:-4.53,-4.84,-15.17:3.06	0/0:7:-1.41,-2.12,-18.82:7.14	0/0:9:-0.02,-2.72,-26.42:27.00	0/0:4:-0.02,-1.22,-12.21:11.96	0/0:2:-0.01,-0.61,-5.73:6.00	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-13.11:12.03	0/0:2:-0.00,-0.60,-7.03:6.02	0/0:4:-0.01,-1.21,-12.87:12.00	0/0:8:-0.05,-2.44,-23.58:23.90	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.53:6.02	0/0:2:-0.00,-0.60,-6.69:6.02	0/1:2:-2.81,-0.60,-2.14:15.35	0/0:3:-0.00,-0.90,-10.03:9.02	0/0:6:-0.06,-1.83,-16.24:17.72	0/0:4:-0.00,-1.20,-12.96:12.03	./.:-1:0,0,0:-1	0/0:1:-1.37,-1.59,-2.05:2.18	0/0:4:-0.01,-1.21,-11.77:12.01	0/1:6:-4.61,-1.81,-12.12:27.95	0/0:6:-0.01,-1.81,-17.84:18.02	0/1:3:-1.50,-0.91,-6.20:5.90	0/0:4:-0.00,-1.21,-13.07:12.03	0/0:1:-0.00,-0.30,-3.34:3.01	0/0:2:-0.00,-0.60,-5.98:6.01	0/1:2:-2.10,-0.61,-2.34:14.99	0/0:3:-0.05,-0.92,-7.22:8.75	0/0:7:-1.91,-2.11,-19.02:2.06	0/0:1:-0.01,-0.31,-1.84:2.95	0/0:2:-0.00,-0.60,-6.78:6.02	0/0:4:-0.01,-1.21,-12.02:12.02	0/1:4:-2.20,-1.21,-9.52:9.96	0/0:3:-0.04,-0.93,-7.63:8.90	./.:-1:0,0,0:-1	0/0:7:-1.72,-2.12,-17.36:4.00	0/0:1:-0.00,-0.30,-3.54:3.01	0/0:3:-0.00,-0.90,-9.43:9.02	0/0:3:-0.00,-0.91,-8.77:9.01	0/0:3:-0.00,-0.90,-9.83:9.02	0/0:10:-0.05,-3.04,-30.20:29.92	0/0:13:-2.12,-3.93,-37.75:18.07
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-20	61809	.	T	C	28.51	0	AB=0.50;AC=1;AF=0.01;AN=98;DB=0;DP=151;Dels=0.00;HRun=0;HaplotypeScore=24.29;MQ=56.95;MQ0=0;OQ=21.95;QD=5.49;SB=-505.67	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-7.51:6.02	0/0:6:-0.00,-1.81,-22.35:18.06	0/0:6:-0.01,-1.81,-21.30:18.05	0/0:1:-0.00,-0.30,-3.86:3.01	0/0:1:-0.00,-0.30,-3.47:3.01	0/0:2:-0.00,-0.60,-7.61:6.02	0/0:4:-0.00,-1.21,-15.65:12.04	0/0:1:-0.00,-0.30,-3.86:3.01	0/0:2:-0.02,-0.62,-5.93:5.99	0/1:3:-6.66,-0.90,-3.96:30.53	0/0:2:-0.01,-0.61,-6.23:6.00	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:2:-0.00,-0.60,-7.31:6.02	0/0:4:-0.00,-1.21,-15.32:12.04	0/0:2:-0.00,-0.60,-6.83:6.02	0/0:1:-0.00,-0.30,-3.67:3.01	0/0:2:-0.00,-0.60,-7.82:6.02	0/0:6:-0.00,-1.81,-22.13:18.06	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:4:-0.00,-1.21,-14.35:12.04	0/0:2:-0.00,-0.60,-7.33:6.02	0/0:8:-0.01,-2.41,-28.08:24.07	0/0:3:-0.01,-0.91,-9.99:9.02	0/0:4:-0.00,-1.21,-14.82:12.04	0/0:1:-0.00,-0.30,-3.57:3.01	0/0:4:-0.02,-1.22,-13.25:12.01	0/0:3:-0.02,-0.92,-8.79:9.00	0/0:2:-1.74,-2.11,-5.76:3.72	0/0:4:-0.00,-1.21,-15.03:12.04	0/0:6:-0.01,-1.82,-20.65:18.03	0/0:2:-0.01,-0.61,-6.03:6.00	0/0:4:-0.00,-1.21,-14.65:12.04	0/0:2:-0.00,-0.60,-7.12:6.02	./.:-1:0,0,0:-1	0/0:2:-0.02,-0.62,-4.82:5.98	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.42:6.02	0/0:5:-0.00,-1.51,-18.10:15.05	0/0:6:-0.01,-1.82,-20.38:18.04	0/0:5:-0.00,-1.51,-17.50:15.04	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-13.85:12.03	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:2:-0.00,-0.60,-7.21:6.02	0/0:3:-0.00,-0.90,-10.48:9.03	0/0:1:-0.00,-0.30,-3.57:3.01	0/0:5:-0.00,-1.51,-18.01:15.05
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-20	62209	.	C	A	0.00	FDRtranche25.00to35.00+	AB=0.67;AC=4;AF=0.05;AN=98;DB=0;DP=107;Dels=0.00;HRun=4;HaplotypeScore=8.55;MQ=58.55;MQ0=0;OQ=24.75;QD=1.55;SB=-398.21	GT:DP:GL:GQ	0/0:3:-0.00,-0.90,-8.86:9.01	0/0:2:-0.00,-0.60,-6.50:6.02	0/0:1:-0.00,-0.30,-2.86:3.00	0/0:2:-0.00,-0.60,-5.80:6.01	0/0:2:-0.00,-0.60,-6.10:6.01	0/0:2:-0.00,-0.60,-6.76:6.02	0/0:2:-0.00,-0.60,-6.60:6.02	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:2:-0.00,-0.60,-5.91:6.01	0/0:2:-0.00,-0.60,-6.30:6.01	0/0:2:-0.01,-0.61,-5.66:6.00	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.52:9.02	0/0:5:-0.01,-1.51,-14.62:14.97	0/0:5:-0.01,-1.51,-15.12:15.02	0/0:3:-0.00,-0.90,-9.56:9.02	0/0:4:-0.05,-1.22,-10.26:11.73	0/0:2:-0.00,-0.60,-5.70:6.00	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.00:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.76:6.01	0/1:3:-3.30,-0.90,-6.46:23.92	0/1:3:-1.90,-0.92,-4.62:9.84	0/0:1:-0.00,-0.30,-3.20:3.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.10:3.01	0/0:3:-0.01,-0.91,-8.36:8.99	0/0:1:-0.00,-0.30,-3.26:3.01	0/1:6:-2.21,-1.82,-14.07:3.91	0/0:2:-0.00,-0.60,-6.36:6.01	0/0:1:-0.01,-0.31,-1.80:2.94	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:1:-0.00,-0.30,-3.10:3.01	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.01,-0.61,-5.06:5.95	0/0:5:-1.60,-1.53,-12.71:2.69	0/1:3:-3.40,-0.90,-6.16:24.92	0/0:2:-0.00,-0.60,-5.56:6.00	0/0:1:-0.00,-0.30,-2.30:2.99	./.:-1:0,0,0:-1	0/0:2:-0.05,-0.62,-3.90:5.72	0/0:2:-0.01,-0.61,-4.81:5.98	0/0:3:-0.03,-0.92,-6.92:8.90	0/0:3:-0.00,-0.90,-9.10:9.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.50:3.00
-20	62555	.	C	A	0.71	FDRtranche25.00to35.00+	AB=0.65;AC=3;AF=0.03;AN=98;DB=0;DP=145;Dels=0.00;HRun=0;HaplotypeScore=10.83;MQ=50.97;MQ0=2;OQ=29.89;QD=2.99;SB=-521.60	GT:DP:GL:GQ	0/0:4:-0.01,-1.21,-12.27:12.01	0/1:4:-3.26,-1.21,-8.16:20.49	0/0:2:-0.00,-0.60,-6.86:6.02	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:7:-0.01,-2.11,-22.19:21.05	0/0:1:-0.00,-0.30,-2.90:3.00	0/0:2:-0.00,-0.60,-6.21:6.01	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:4:-0.00,-1.21,-13.37:12.03	0/0:3:-0.00,-0.90,-9.66:9.02	0/0:1:-0.00,-0.30,-3.40:3.01	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:2:-0.00,-0.60,-6.30:6.01	0/0:3:-0.00,-0.90,-9.92:9.02	0/0:5:-0.04,-1.53,-13.53:14.91	0/0:2:-0.00,-0.60,-6.26:6.01	0/0:1:-0.00,-0.30,-3.30:3.01	0/1:4:-3.46,-1.24,-5.46:22.19	0/0:1:-0.00,-0.30,-3.06:3.01	0/0:4:-0.00,-1.21,-12.20:12.02	0/0:3:-0.00,-0.90,-9.90:9.02	0/0:5:-0.00,-1.51,-15.02:15.03	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:4:-0.00,-1.21,-12.42:12.03	0/0:3:-0.00,-0.90,-9.66:9.02	0/1:2:-3.30,-0.60,-3.26:26.55	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:1:-0.00,-0.30,-2.30:2.99	0/0:2:-0.00,-0.60,-6.10:6.01	0/0:1:-0.00,-0.30,-3.16:3.01	0/0:5:-0.00,-1.51,-16.72:15.04	0/0:5:-0.01,-1.51,-14.72:15.00	0/0:2:-0.00,-0.60,-5.50:6.00	0/0:5:-0.01,-1.51,-14.52:15.01	0/0:5:-0.04,-1.53,-14.22:14.91	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.46:9.02	0/0:4:-0.00,-1.21,-12.62:12.03	0/0:4:-0.00,-1.21,-12.06:12.02	0/0:3:-0.02,-0.92,-7.66:8.94	0/0:1:-0.01,-0.31,-1.80:2.94	0/0:2:-0.00,-0.60,-6.46:6.02	0/0:2:-0.00,-0.60,-6.76:6.02	0/0:2:-0.01,-0.60,-5.36:5.99	0/0:4:-0.00,-1.21,-11.96:12.02	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:3:-0.01,-0.91,-7.50:8.97	0/0:2:-0.00,-0.60,-6.81:6.02
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-20	67955	.	G	A	0.01	FDRtranche25.00to35.00+	AB=0.55;AC=4;AF=0.05;AN=98;DB=0;DP=163;Dels=0.00;HRun=2;HaplotypeScore=59.71;MQ=57.38;MQ0=0;OQ=18.42;QD=0.74;SB=-432.97	GT:DP:GL:GQ	0/0:1:-0.01,-0.31,-2.20:2.98	0/0:3:-0.02,-0.91,-8.63:8.93	0/0:2:-0.00,-0.60,-6.96:6.02	0/0:1:-0.00,-0.30,-2.67:3.00	0/0:3:-0.02,-0.91,-7.06:8.96	0/0:4:-0.05,-1.23,-9.66:11.82	./.:-1:0,0,0:-1	0/0:4:-0.01,-1.21,-12.56:12.02	0/0:1:-0.00,-0.30,-3.00:3.01	0/0:1:-0.00,-0.30,-2.60:3.00	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.63:9.02	0/1:3:-2.41,-2.18,-5.47:2.30	0/0:1:-0.00,-0.30,-3.27:3.01	0/1:4:-3.67,-1.21,-8.96:24.59	0/0:6:-0.01,-1.81,-19.45:18.04	0/1:3:-1.86,-0.93,-7.12:9.31	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:2:-0.01,-0.61,-5.59:6.00	0/0:2:-0.00,-0.60,-6.36:6.01	0/0:3:-0.05,-0.93,-7.36:8.76	0/0:1:-0.00,-0.30,-3.60:3.01	0/0:3:-0.00,-0.90,-9.03:9.01	0/0:2:-0.00,-0.60,-6.46:6.01	0/0:7:-0.03,-2.12,-19.39:20.94	0/0:1:-0.00,-0.30,-2.97:3.01	0/0:2:-0.01,-0.61,-4.99:5.98	0/0:1:-0.00,-0.30,-3.50:3.01	0/1:3:-4.75,-2.80,-5.01:19.51	0/0:3:-0.00,-0.91,-9.66:9.01	0/0:3:-0.00,-0.90,-10.09:9.02	0/0:4:-0.02,-1.21,-12.56:11.99	0/0:2:-0.00,-0.60,-7.59:6.02	0/0:5:-0.00,-1.51,-17.25:15.04	0/0:3:-0.01,-0.91,-8.26:8.96	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.43:9.02	0/0:3:-0.00,-0.91,-9.49:9.02	0/0:1:-0.00,-0.30,-2.77:3.00	0/0:5:-0.02,-1.52,-14.38:14.97	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-8.99:9.01	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:3:-0.00,-0.90,-10.69:9.03	0/0:3:-0.01,-0.91,-9.26:8.97	0/0:5:-0.02,-1.51,-14.03:14.99	0/0:3:-0.00,-0.90,-10.29:9.03
-20	68170	.	C	T	0.74	FDRtranche25.00to35.00+	AB=0.40;AC=2;AF=0.02;AN=98;DB=0;DP=178;Dels=0.00;HRun=0;HaplotypeScore=24.31;MQ=57.58;MQ0=0;OQ=13.19;QD=2.64;SB=-506.46	GT:DP:GL:GQ	0/1:2:-4.07,-0.60,-3.10:24.93	0/0:3:-0.00,-0.90,-9.51:9.02	0/1:2:-2.26,-0.61,-2.91:16.46	0/0:4:-0.01,-1.21,-11.73:12.02	0/0:2:-0.00,-0.60,-6.04:6.01	0/0:2:-0.00,-0.60,-5.94:6.01	0/0:2:-0.00,-0.60,-5.56:6.01	0/0:5:-0.03,-1.52,-12.15:14.96	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.97:3.01	0/0:2:-0.00,-0.60,-6.54:6.02	0/0:1:-0.00,-0.30,-3.17:3.01	0/0:2:-0.01,-0.61,-4.96:5.98	0/0:2:-0.00,-0.60,-6.26:6.01	0/0:2:-0.00,-0.60,-6.04:6.01	0/0:5:-0.01,-1.51,-14.50:15.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.34:6.00	0/0:6:-0.02,-1.82,-15.67:17.98	0/0:5:-0.01,-1.51,-14.50:15.02	0/0:4:-0.02,-1.21,-10.97:11.95	0/0:6:-0.01,-1.81,-16.17:18.01	0/0:3:-0.00,-0.91,-8.63:9.01	0/0:2:-0.00,-0.60,-5.84:6.01	0/0:3:-0.00,-0.90,-8.61:9.01	0/0:1:-0.00,-0.30,-2.80:3.00	0/0:3:-0.00,-0.90,-9.46:9.02	0/0:4:-0.01,-1.21,-11.83:12.02	0/0:3:-0.00,-0.91,-8.43:9.01	0/0:4:-0.02,-1.22,-10.73:11.97	0/0:7:-0.03,-2.13,-20.16:20.98	0/0:3:-0.00,-0.91,-8.86:9.01	0/0:2:-0.00,-0.60,-6.24:6.01	0/0:2:-0.00,-0.60,-5.56:6.00	0/0:2:-0.01,-0.61,-5.79:6.00	0/0:9:-0.03,-2.73,-24.50:26.96	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.97:3.01	0/0:7:-0.03,-2.13,-18.79:20.97	0/0:5:-0.01,-1.51,-13.57:14.99	0/0:2:-0.00,-0.60,-5.76:6.01	0/0:1:-0.00,-0.30,-2.97:3.01	0/0:6:-0.02,-1.82,-16.17:17.98	0/0:6:-0.01,-1.81,-18.54:18.04	0/0:3:-0.00,-0.91,-8.93:9.02	0/0:4:-0.00,-1.21,-11.87:12.02	0/0:2:-0.00,-0.60,-6.04:6.01	0/0:7:-0.03,-2.12,-19.26:20.94	0/0:6:-0.06,-1.84,-15.67:17.86
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-20	73200	.	A	G	0.53	FDRtranche25.00to35.00+	AB=0.75;AC=2;AF=0.03;AN=98;DB=0;DP=160;Dels=0.00;HRun=0;HaplotypeScore=14.53;MQ=35.80;MQ0=17;OQ=13.49;QD=2.70;SB=-457.00	GT:DP:GL:GQ	0/0:3:-0.00,-0.91,-10.49:9.03	0/0:3:-0.03,-0.93,-9.59:8.98	0/0:3:-0.01,-0.92,-9.99:9.01	0/0:3:-0.02,-0.92,-9.77:8.98	0/0:2:-0.01,-0.61,-5.92:6.01	1/1:1:-3.27,-0.30,-0.00:3.01	0/0:4:-0.04,-1.24,-11.75:11.97	0/0:5:-0.00,-1.51,-18.60:15.05	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-14.75:12.04	0/0:4:-0.00,-1.21,-14.05:12.03	0/0:3:-0.00,-0.90,-10.88:9.03	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-15.16:12.04	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:1:-0.00,-0.30,-3.76:3.01	0/0:2:-0.00,-0.60,-7.13:6.02	0/0:6:-0.02,-1.83,-19.49:18.02	0/0:2:-0.01,-0.61,-5.82:6.00	0/0:1:-0.00,-0.30,-2.96:3.01	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.32:6.02	0/0:1:-0.00,-0.30,-3.06:3.01	0/0:2:-0.00,-0.60,-7.51:6.02	0/0:6:-0.01,-1.81,-20.98:18.05	0/0:3:-0.00,-0.90,-11.17:9.03	0/0:4:-0.01,-1.21,-14.36:12.03	0/0:5:-0.01,-1.52,-16.50:15.03	0/0:2:-0.00,-0.60,-7.21:6.02	0/0:2:-0.00,-0.60,-7.92:6.02	0/0:2:-0.00,-0.60,-8.02:6.02	./.:-1:0,0,0:-1	0/0:3:-0.02,-0.92,-9.78:9.00	0/0:2:-0.00,-0.60,-7.61:6.02	0/0:2:-0.00,-0.60,-7.11:6.02	0/0:3:-0.01,-0.91,-9.58:9.01	0/0:1:-0.01,-0.31,-2.37:2.99	0/0:1:-0.00,-0.30,-3.77:3.01	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:1:-0.00,-0.30,-3.87:3.01	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:5:-0.00,-1.51,-19.18:15.05	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:1:-0.00,-0.30,-3.17:3.01	0/0:4:-0.00,-1.21,-14.57:12.04	0/0:4:-0.00,-1.21,-14.52:12.04	0/0:6:-0.05,-1.85,-19.17:17.97
-20	73857	.	G	A	21.56	0	AB=0.40;AC=1;AF=0.01;AN=98;DB=0;DP=153;Dels=0.00;HRun=0;HaplotypeScore=20.25;MQ=42.81;MQ0=17;OQ=32.73;QD=6.55;SB=-420.00	GT:DP:GL:GQ	0/0:5:-0.01,-1.51,-14.23:15.01	0/0:3:-0.00,-0.90,-8.81:9.01	./.:-1:0,0,0:-1	0/0:2:-0.01,-0.61,-5.39:6.00	0/0:3:-0.00,-0.91,-8.73:9.01	0/0:1:-0.00,-0.30,-3.10:3.01	0/0:3:-0.00,-0.91,-9.03:9.02	0/0:8:-0.02,-2.42,-21.36:23.98	0/0:2:-0.01,-0.61,-5.46:5.99	0/0:8:-0.05,-2.44,-20.99:23.92	0/0:4:-0.01,-1.21,-11.73:12.02	0/0:5:-0.01,-1.51,-14.35:15.01	0/0:1:-0.00,-0.30,-3.40:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.56:6.01	0/0:2:-0.00,-0.60,-5.46:6.00	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:4:-0.03,-1.22,-9.28:11.95	0/0:1:-0.00,-0.30,-2.80:3.00	0/0:2:-0.02,-0.62,-4.19:5.95	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/1:3:-7.73,-0.90,-3.40:24.93	0/0:1:-0.00,-0.30,-2.80:3.00	0/0:4:-0.02,-1.22,-10.18:11.97	0/0:3:-0.02,-0.92,-7.46:8.97	0/0:2:-0.00,-0.61,-5.59:6.01	0/0:1:-0.00,-0.30,-2.87:3.00	0/0:3:-0.01,-0.91,-8.16:8.99	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-8.19:9.00	0/0:4:-0.01,-1.21,-11.86:12.02	0/0:5:-0.02,-1.52,-14.05:15.00	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:3:-0.01,-0.91,-7.89:9.00	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-7.69:8.99	0/0:2:-0.00,-0.60,-6.14:6.01	0/0:3:-0.01,-0.91,-7.89:9.00	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.66:6.01	0/0:1:-0.00,-0.30,-2.60:3.00	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.16:6.01	0/0:1:-0.00,-0.30,-2.97:3.01	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.76:6.01	0/0:3:-0.02,-0.92,-7.66:8.96
-20	73862	.	G	A	3.38	FDRtranche12.50to25.00	AB=0.60;AC=1;AF=0.01;AN=98;DB=0;DP=158;Dels=0.00;HRun=1;HaplotypeScore=21.38;MQ=45.42;MQ0=13;OQ=26.56;QD=5.31;SB=-488.66	GT:DP:GL:GQ	0/1:5:-7.73,-1.51,-8.26:62.19	0/0:2:-0.00,-0.60,-6.24:6.01	./.:-1:0,0,0:-1	0/0:2:-0.04,-0.63,-3.69:5.88	0/0:4:-0.02,-1.22,-10.53:11.98	0/0:1:-0.00,-0.30,-2.90:3.00	0/0:3:-0.01,-0.91,-7.93:8.97	0/0:9:-0.02,-2.72,-24.65:26.99	0/0:1:-0.00,-0.30,-3.47:3.01	0/0:9:-0.02,-2.72,-24.98:27.01	0/0:2:-0.00,-0.60,-5.89:6.01	0/0:3:-0.01,-0.91,-8.16:9.01	0/0:1:-0.00,-0.30,-2.80:3.00	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-8.83:9.01	0/0:2:-0.01,-0.61,-4.99:5.99	0/0:1:-0.00,-0.30,-3.37:3.01	0/0:5:-0.02,-1.52,-13.48:14.99	0/0:2:-0.00,-0.61,-5.59:6.01	0/0:2:-0.01,-0.61,-5.09:5.99	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-12.16:12.02	0/0:3:-0.01,-0.91,-7.79:8.99	0/0:1:-0.00,-0.30,-2.70:3.00	0/0:5:-0.03,-1.52,-13.45:14.96	0/0:3:-0.01,-0.91,-8.43:9.00	0/0:2:-0.00,-0.61,-5.49:6.00	0/0:2:-0.00,-0.60,-6.24:6.01	0/0:3:-0.05,-0.94,-7.46:8.87	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:2:-0.00,-0.60,-5.69:6.01	0/0:4:-0.01,-1.21,-10.86:12.00	0/0:5:-0.04,-1.53,-12.55:14.91	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:3:-0.01,-0.91,-8.39:9.01	./.:-1:0,0,0:-1	0/0:4:-0.02,-1.21,-10.28:11.99	0/0:2:-0.00,-0.60,-5.94:6.01	0/0:3:-0.02,-0.91,-7.49:8.98	0/0:1:-0.00,-0.30,-2.60:3.00	0/0:2:-0.00,-0.60,-5.86:6.01	0/0:1:-0.01,-0.31,-2.30:2.99	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-12.70:12.03	0/0:2:-0.01,-0.61,-5.26:6.00	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-8.66:9.01	0/0:2:-0.00,-0.60,-5.86:6.01	0/0:4:-0.01,-1.21,-11.73:12.02
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-20	80305	.	A	G	0.21	FDRtranche25.00to35.00+	AB=0.53;AC=13;AF=0.15;AN=98;DB=0;DP=125;Dels=0.00;HRun=1;HaplotypeScore=58.36;MQ=55.01;MQ0=0;OQ=143.13;QD=4.47;SB=-400.73	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-7.81:6.02	0/1:5:-1.60,-1.53,-15.96:0.67	0/1:2:-2.50,-0.61,-3.86:18.91	0/0:2:-0.00,-0.60,-7.12:6.02	0/0:1:-0.00,-0.30,-3.27:3.01	1/1:1:-1.50,-0.33,-0.05:2.86	0/0:1:-0.00,-0.30,-3.56:3.01	0/0:2:-0.00,-0.60,-7.51:6.02	0/0:1:-0.00,-0.30,-3.96:3.01	0/0:2:-0.00,-0.60,-7.51:6.02	0/0:1:-0.00,-0.30,-3.46:3.01	0/1:3:-2.70,-0.91,-7.81:17.91	0/0:1:-0.00,-0.30,-3.76:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-11.18:9.03	0/0:4:-1.96,-3.04,-12.73:10.81	0/1:2:-2.00,-0.61,-3.97:13.85	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-11.27:9.03	0/0:2:-0.01,-0.61,-5.92:6.00	0/0:3:-0.03,-0.93,-8.30:8.98	0/0:1:-1.64,-1.71,-1.79:0.71	0/0:1:-0.00,-0.30,-2.76:3.00	0/1:4:-4.10,-1.23,-6.75:28.71	0/1:2:-3.70,-0.60,-3.86:30.94	0/1:2:-1.50,-0.63,-3.90:8.64	0/0:4:-0.01,-1.21,-12.42:12.02	0/0:1:-0.00,-0.30,-3.76:3.01	0/0:3:-0.01,-0.91,-9.97:9.02	0/0:3:-0.00,-0.90,-11.28:9.03	0/0:2:-0.03,-0.63,-5.92:5.97	0/0:3:-0.00,-0.91,-10.48:9.02	0/0:4:-0.00,-1.21,-14.43:12.03	0/0:1:-0.00,-0.30,-3.76:3.01	0/0:2:-0.00,-0.60,-7.21:6.02	0/0:2:-0.00,-0.60,-6.82:6.02	0/0:2:-0.00,-0.60,-7.81:6.02	0/1:2:-1.50,-0.63,-3.60:8.64	0/0:2:-0.00,-0.60,-7.51:6.02	1/1:1:-3.10,-0.30,-0.00:3.01	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.22:6.02	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:4:-0.02,-1.22,-12.06:12.01	0/0:3:-0.00,-0.91,-10.18:9.02	0/1:3:-2.00,-0.91,-7.54:10.84
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-20	83196	rs62190472	A	T	0.78	FDRtranche25.00to35.00+	AB=0.60;AC=1;AF=0.01;AN=98;DB=1;DP=146;Dels=0.00;HRun=1;HaplotypeScore=20.91;MQ=56.21;MQ0=0;OQ=14.83;QD=2.97;SB=-482.38	GT:DP:GL:GQ	0/0:6:-0.01,-1.82,-19.75:18.03	0/0:3:-0.00,-0.90,-10.58:9.03	0/0:1:-0.00,-0.30,-2.90:3.00	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-9.24:9.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.54:3.01	0/0:6:-0.01,-1.82,-18.69:18.02	0/0:2:-0.00,-0.60,-6.04:6.00	0/0:5:-0.00,-1.51,-17.46:15.04	0/0:5:-0.00,-1.51,-16.63:15.04	0/0:2:-0.01,-0.61,-5.50:6.00	0/0:2:-0.01,-0.61,-5.34:5.98	0/0:3:-0.00,-0.91,-9.84:9.02	0/0:4:-0.01,-1.21,-12.52:12.02	0/0:3:-0.01,-0.91,-9.44:9.01	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-9.60:9.02	0/0:2:-0.00,-0.60,-6.74:6.02	0/0:1:-0.00,-0.30,-2.70:3.00	0/0:1:-0.00,-0.30,-3.34:3.01	0/0:3:-0.00,-0.90,-10.14:9.03	0/0:4:-0.00,-1.21,-13.58:12.03	0/0:2:-0.00,-0.60,-6.84:6.02	0/0:4:-0.00,-1.21,-13.92:12.04	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.68:6.02	0/0:4:-0.00,-1.21,-13.42:12.03	0/0:1:-0.00,-0.30,-3.44:3.01	0/0:3:-0.00,-0.90,-10.22:9.03	0/0:4:-0.00,-1.21,-13.38:12.03	0/0:2:-0.00,-0.60,-7.04:6.02	0/0:1:-0.00,-0.30,-3.60:3.01	0/0:1:-0.00,-0.30,-3.60:3.01	0/0:4:-0.02,-1.22,-12.48:11.99	0/0:2:-0.01,-0.61,-5.70:5.99	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:2:-0.00,-0.60,-6.94:6.02	0/0:2:-0.00,-0.60,-5.74:6.01	0/1:5:-6.54,-1.51,-9.44:50.33	0/0:3:-0.03,-0.92,-8.48:8.90	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.74:6.02	0/0:1:-0.00,-0.30,-3.70:3.01	0/0:1:-0.00,-0.30,-3.44:3.01	0/0:5:-0.00,-1.51,-16.10:15.04	0/0:4:-0.00,-1.21,-13.46:12.03	0/0:4:-0.00,-1.21,-13.28:12.03	0/0:4:-0.00,-1.21,-13.06:12.03
-20	83250	.	C	G	588.28	HARD_TO_VALIDATE;SnpCluster	AB=0.65;AC=16;AF=0.17;AN=98;DB=0;DP=185;Dels=0.00;HRun=0;HaplotypeScore=86.04;MQ=36.61;MQ0=48;QD=10.89;SB=-677.25	GT:DP:GL:GQ	1/1:2:-8.04,-0.60,-0.00:6.02	0/0:2:-0.00,-0.60,-8.68:6.02	0/0:3:-0.01,-0.91,-10.49:9.03	0/1:2:-3.95,-0.60,-4.15:33.45	0/0:5:-0.00,-1.51,-20.37:15.05	0/1:4:-12.73,-1.21,-3.59:23.86	0/0:5:-0.00,-1.51,-21.13:15.05	0/0:4:-0.00,-1.21,-15.78:12.04	./.:-1:0,0,0:-1	0/0:5:-0.00,-1.51,-20.87:15.05	0/1:4:-8.15,-1.21,-7.34:61.30	0/0:3:-0.00,-0.90,-12.63:9.03	0/0:2:-0.01,-0.61,-7.08:6.01	0/0:1:-0.00,-0.30,-4.49:3.01	./.:-1:0,0,0:-1	0/1:4:-3.65,-1.21,-12.13:24.42	0/0:1:-0.00,-0.30,-3.85:3.01	0/0:5:-0.04,-1.54,-19.02:15.01	0/0:4:-0.00,-1.21,-15.09:12.04	0/0:3:-0.00,-0.91,-11.19:9.03	0/0:1:-0.00,-0.30,-4.09:3.01	0/1:6:-6.54,-1.82,-16.44:47.22	0/0:3:-0.01,-0.92,-11.48:9.02	0/1:4:-3.39,-1.21,-12.58:21.85	0/0:3:-0.01,-0.91,-11.63:9.03	0/1:3:-3.75,-0.90,-7.94:28.43	0/0:4:-0.00,-1.21,-16.18:12.04	0/1:4:-5.89,-1.23,-8.17:46.64	0/1:2:-3.65,-0.60,-4.39:30.44	0/0:3:-0.00,-0.90,-12.63:9.03	0/0:2:-0.00,-0.60,-8.68:6.02	0/0:3:-0.00,-0.90,-13.28:9.03	0/0:1:-0.00,-0.30,-3.85:3.01	1/1:2:-7.09,-0.60,-0.00:6.02	0/0:3:-0.00,-0.91,-11.83:9.03	0/0:2:-0.00,-0.60,-8.38:6.02	0/1:2:-3.65,-0.60,-4.19:30.44	0/0:1:-0.00,-0.30,-4.19:3.01	1/1:1:-3.45,-0.30,-0.00:3.01	0/0:5:-0.00,-1.51,-20.82:15.05	0/0:2:-0.00,-0.60,-7.94:6.02	0/0:1:-0.00,-0.30,-4.29:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-8.54:6.02	0/0:1:-0.02,-0.32,-2.59:3.00	0/0:3:-0.00,-0.90,-12.43:9.03	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.91,-11.59:9.03	0/0:2:-0.00,-0.60,-8.58:6.02
-20	83252	rs6137896	G	C	1331.58	HARD_TO_VALIDATE;SnpCluster	AB=0.66;AC=25;AF=0.31;AN=98;DB=1;DP=186;Dels=0.00;HRun=0;HaplotypeScore=54.04;MQ=33.89;MQ0=61;QD=12.68;SB=-1062.43	GT:DP:GL:GQ	0/0:2:-0.01,-0.61,-6.69:6.01	1/1:2:-8.58,-0.60,-0.00:6.02	0/1:3:-7.40,-0.91,-3.15:22.42	0/1:2:-3.15,-0.60,-3.85:25.42	0/1:5:-16.28,-1.51,-3.55:20.41	0/0:4:-0.01,-1.21,-15.68:12.03	0/1:4:-12.29,-1.21,-4.59:33.88	1/1:4:-15.28,-1.21,-0.00:12.04	./.:-1:0,0,0:-1	0/1:5:-11.81,-1.52,-5.20:36.71	0/1:3:-3.15,-0.91,-7.74:22.42	0/1:2:-4.29,-0.60,-3.35:27.43	0/0:2:-0.03,-0.63,-4.99:5.99	0/0:1:-0.00,-0.30,-4.05:3.01	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-15.43:12.04	0/0:1:-0.00,-0.30,-4.59:3.01	0/0:1:-0.04,-0.34,-2.39:2.99	0/1:4:-10.64,-1.21,-4.40:31.88	0/0:3:-0.00,-0.91,-12.03:9.03	./.:-1:0,0,0:-1	0/0:5:-0.01,-1.51,-17.63:15.04	0/0:3:-0.00,-0.90,-11.44:9.03	0/1:4:-3.90,-1.21,-11.59:26.88	1/1:3:-12.73,-0.90,-0.00:9.03	0/0:3:-0.00,-0.91,-11.29:9.03	0/1:4:-3.78,-1.24,-9.69:25.47	0/0:3:-0.00,-0.91,-11.09:9.03	0/0:2:-0.00,-0.60,-7.29:6.02	0/1:2:-4.29,-0.60,-4.49:36.90	0/1:2:-4.30,-0.61,-2.55:19.35	0/1:3:-4.60,-0.91,-6.79:36.90	0/0:1:-0.00,-0.30,-3.99:3.01	0/0:1:-0.00,-0.30,-2.95:3.01	0/1:4:-3.46,-1.22,-10.19:22.42	1/1:1:-4.29,-0.30,-0.00:3.01	0/0:2:-0.00,-0.60,-7.19:6.02	0/0:1:-0.00,-0.30,-3.95:3.01	0/0:1:-0.00,-0.30,-3.65:3.01	0/1:5:-4.32,-1.53,-14.23:27.90	0/0:2:-0.00,-0.60,-7.94:6.02	0/0:1:-0.00,-0.30,-2.95:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.74:6.02	0/0:1:-0.00,-0.30,-3.75:3.01	0/1:3:-3.75,-0.91,-6.99:28.43	./.:-1:0,0,0:-1	0/0:3:-0.04,-0.94,-9.93:9.01	0/1:2:-4.29,-0.60,-3.45:28.44
-20	83254	.	G	C	152.46	HARD_TO_VALIDATE;SnpCluster	AB=0.72;AC=4;AF=0.07;AN=98;DB=0;DP=189;Dels=0.00;HRun=0;HaplotypeScore=76.76;MQ=32.47;MQ0=68;QD=6.93;SB=-516.76	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-7.84:6.02	0/0:2:-0.00,-0.60,-7.19:6.02	0/1:3:-7.19,-0.91,-3.85:29.44	0/0:2:-0.00,-0.60,-8.44:6.02	0/0:6:-0.00,-1.81,-23.37:18.06	0/0:4:-0.00,-1.21,-16.78:12.04	0/1:4:-3.55,-1.21,-12.43:23.42	0/0:3:-0.01,-0.91,-10.29:9.02	./.:-1:0,0,0:-1	0/0:5:-0.01,-1.51,-19.33:15.05	0/0:3:-0.01,-0.91,-11.13:9.02	0/0:2:-0.00,-0.60,-6.99:6.02	0/0:2:-0.00,-0.60,-6.99:6.02	0/0:1:-0.00,-0.30,-4.05:3.01	./.:-1:0,0,0:-1	0/0:4:-0.01,-1.22,-14.03:12.03	0/0:1:-0.00,-0.30,-4.69:3.01	0/0:1:-0.01,-0.31,-2.79:3.00	0/0:4:-0.00,-1.21,-17.07:12.04	0/0:3:-0.00,-0.91,-12.03:9.03	./.:-1:0,0,0:-1	0/0:5:-0.01,-1.51,-18.23:15.04	0/0:3:-0.00,-0.91,-11.14:9.03	0/0:4:-0.00,-1.21,-15.03:12.04	0/0:3:-0.00,-0.91,-11.19:9.03	0/0:3:-0.00,-0.90,-11.79:9.03	0/0:4:-0.00,-1.21,-15.68:12.04	0/0:3:-0.00,-0.90,-11.89:9.03	0/0:1:-0.00,-0.30,-3.85:3.01	0/1:2:-4.09,-0.60,-4.39:34.90	0/0:2:-0.00,-0.60,-7.49:6.02	0/0:3:-0.00,-0.91,-11.14:9.03	0/0:1:-0.00,-0.30,-4.19:3.01	0/0:1:-0.00,-0.30,-3.75:3.01	0/0:3:-0.01,-0.91,-10.59:9.03	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.29:6.02	0/0:1:-0.00,-0.30,-3.85:3.01	0/0:1:-0.00,-0.30,-3.55:3.01	0/0:5:-0.01,-1.51,-17.88:15.04	0/0:2:-0.00,-0.60,-8.04:6.02	0/0:1:-0.00,-0.30,-3.75:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-8.24:6.02	0/0:1:-0.00,-0.30,-3.65:3.01	0/1:3:-3.85,-0.90,-7.39:29.44	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-11.13:9.03	0/0:2:-0.00,-0.60,-7.49:6.02
-20	83260	.	G	C	48.53	HARD_TO_VALIDATE;SnpCluster	AB=0.81;AC=2;AF=0.02;AN=98;DB=0;DP=180;Dels=0.00;HRun=0;HaplotypeScore=73.15;MQ=26.89;MQ0=77;QD=2.55;SB=-420.97	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-8.54:6.02	0/0:1:-0.00,-0.30,-3.55:3.01	0/0:3:-0.04,-0.94,-10.29:8.99	0/0:2:-0.00,-0.60,-8.44:6.02	0/1:6:-8.19,-1.81,-16.38:63.78	0/0:4:-0.00,-1.21,-16.28:12.04	0/0:4:-0.00,-1.21,-17.12:12.04	0/0:4:-0.01,-1.21,-13.43:12.03	./.:-1:0,0,0:-1	0/1:5:-3.80,-1.51,-15.33:22.86	0/0:2:-0.00,-0.60,-7.84:6.02	0/0:1:-0.00,-0.30,-3.35:3.01	0/0:2:-0.00,-0.61,-6.59:6.02	0/0:1:-0.00,-0.30,-4.05:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.91,-10.89:9.03	0/0:1:-0.00,-0.30,-4.69:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.91,-11.88:9.03	0/0:3:-0.00,-0.91,-11.83:9.03	./.:-1:0,0,0:-1	0/0:4:-0.03,-1.23,-13.73:12.01	0/0:3:-0.00,-0.90,-11.34:9.03	0/0:2:-0.00,-0.60,-7.29:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.44:6.02	0/0:4:-0.00,-1.21,-15.18:12.04	0/0:2:-0.00,-0.60,-7.94:6.02	0/0:1:-0.00,-0.30,-3.75:3.01	0/0:1:-0.00,-0.30,-4.29:3.01	0/0:1:-0.00,-0.30,-3.85:3.01	0/0:3:-0.00,-0.91,-10.44:9.03	0/0:1:-0.00,-0.30,-3.89:3.01	0/0:1:-0.00,-0.30,-3.05:3.01	0/0:4:-0.02,-1.23,-13.18:12.03	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.99:6.02	0/0:1:-0.00,-0.30,-3.75:3.01	0/0:1:-0.00,-0.30,-3.55:3.01	0/0:5:-0.01,-1.51,-17.28:15.04	0/0:2:-0.00,-0.60,-7.54:6.02	0/0:1:-0.00,-0.30,-3.65:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-8.04:6.02	0/0:1:-0.00,-0.30,-3.65:3.01	0/0:2:-0.02,-0.62,-5.99:6.00	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.92,-10.93:9.02	0/0:2:-0.00,-0.60,-7.49:6.02
-20	83262	.	G	C	30.20	HARD_TO_VALIDATE;SnpCluster	AB=0.80;AC=1;AF=0.01;AN=98;DB=0;DP=182;Dels=0.00;HRun=0;HaplotypeScore=62.69;MQ=25.76;MQ0=81;QD=3.02;SB=-413.98	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-8.44:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.84:6.02	0/0:2:-0.00,-0.60,-8.34:6.02	0/1:6:-8.39,-1.81,-16.08:65.78	0/0:4:-0.00,-1.21,-16.98:12.04	0/0:4:-0.00,-1.21,-16.92:12.04	0/0:3:-0.00,-0.90,-11.69:9.03	./.:-1:0,0,0:-1	0/0:4:-0.01,-1.21,-14.43:12.04	0/0:2:-0.00,-0.60,-8.04:6.02	0/0:1:-0.00,-0.30,-3.35:3.01	0/0:2:-0.00,-0.61,-6.69:6.02	0/0:1:-0.00,-0.30,-4.05:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-11.69:9.03	0/0:1:-0.00,-0.30,-4.69:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-13.08:9.03	0/0:3:-0.00,-0.91,-11.93:9.03	./.:-1:0,0,0:-1	0/0:4:-0.01,-1.21,-14.43:12.04	0/0:3:-0.00,-0.90,-11.24:9.03	0/0:2:-0.00,-0.60,-7.09:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-8.04:6.02	0/0:4:-0.00,-1.21,-15.58:12.04	0/0:2:-0.00,-0.60,-7.94:6.02	0/0:1:-0.00,-0.30,-3.75:3.01	0/0:1:-0.00,-0.30,-4.29:3.01	0/0:1:-0.00,-0.30,-3.85:3.01	0/0:3:-0.00,-0.91,-11.04:9.03	0/0:1:-0.00,-0.30,-3.59:3.01	0/0:1:-0.00,-0.30,-3.65:3.01	0/0:4:-0.02,-1.22,-13.58:12.03	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.65:3.01	0/0:1:-0.00,-0.30,-3.75:3.01	0/0:1:-0.00,-0.30,-3.55:3.01	0/0:5:-0.01,-1.51,-18.38:15.04	0/0:2:-0.00,-0.60,-7.84:6.02	0/0:1:-0.00,-0.30,-3.75:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-8.54:6.02	0/0:1:-0.00,-0.30,-3.65:3.01	0/0:2:-0.00,-0.60,-7.29:6.02	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-10.53:9.03	0/0:2:-0.00,-0.60,-7.49:6.02
-20	83265	rs6137900	T	C	274.44	HARD_TO_VALIDATE;SnpCluster	AB=0.68;AC=17;AF=0.22;AN=98;DB=1;DP=179;Dels=0.00;HRun=0;HaplotypeScore=27.91;MQ=24.40;MQ0=85;QD=7.22;SB=-494.18	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-7.22:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.73:6.02	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:6:-0.00,-1.81,-22.48:18.06	0/0:4:-0.00,-1.21,-15.35:12.04	0/1:4:-3.07,-1.21,-10.88:18.64	0/0:3:-0.00,-0.90,-11.29:9.03	./.:-1:0,0,0:-1	0/1:4:-1.47,-1.22,-11.23:2.52	0/0:2:-0.00,-0.60,-7.13:6.02	0/0:1:-0.00,-0.30,-4.17:3.01	0/0:2:-0.00,-0.60,-7.43:6.02	1/1:1:-3.00,-0.30,-0.00:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-10.99:9.03	1/1:1:-3.07,-0.30,-0.00:3.01	./.:-1:0,0,0:-1	0/1:2:-2.87,-0.61,-2.76:21.51	0/0:3:-0.00,-0.90,-11.08:9.03	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-14.86:12.04	0/1:3:-5.79,-0.91,-3.87:29.65	0/0:2:-0.00,-0.60,-7.73:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:4:-0.00,-1.21,-15.15:12.04	1/1:2:-5.76,-0.60,-0.00:6.01	1/1:1:-3.00,-0.30,-0.00:3.01	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:1:-0.00,-0.30,-3.47:3.01	0/1:2:-3.00,-0.60,-3.87:23.93	0/0:1:-0.00,-0.30,-3.66:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-11.69:9.03	./.:-1:0,0,0:-1	1/1:1:-2.60,-0.30,-0.00:3.00	0/0:1:-0.00,-0.30,-3.87:3.01	./.:-1:0,0,0:-1	0/0:5:-0.00,-1.51,-18.82:15.05	0/0:2:-0.00,-0.60,-7.62:6.02	1/1:1:-2.80,-0.30,-0.00:3.00	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-8.02:6.02	0/0:1:-0.00,-0.30,-3.77:3.01	0/0:2:-0.00,-0.60,-7.03:6.02	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-10.88:9.03	0/0:2:-0.00,-0.60,-7.73:6.02
-20	83267	.	T	C	61.14	HARD_TO_VALIDATE;SnpCluster	AB=0.67;AC=2;AF=0.03;AN=98;DB=0;DP=175;Dels=0.00;HRun=0;HaplotypeScore=32.45;MQ=23.96;MQ0=87;QD=4.37;SB=-433.32	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-7.12:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.63:6.02	0/0:1:-0.00,-0.30,-3.37:3.01	0/0:5:-0.00,-1.51,-19.02:15.05	0/0:4:-0.00,-1.21,-15.35:12.04	0/1:4:-6.17,-1.21,-7.51:49.60	0/1:3:-5.86,-0.90,-3.97:30.65	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-11.30:9.03	0/0:3:-0.02,-0.92,-9.49:8.98	0/0:1:-0.00,-0.30,-4.17:3.01	0/0:2:-0.00,-0.60,-7.43:6.02	0/0:1:-0.00,-0.30,-2.87:3.00	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-10.69:9.03	0/0:1:-0.00,-0.30,-3.76:3.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.56:3.01	0/0:3:-0.00,-0.90,-11.18:9.03	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.82:6.02	0/0:3:-0.00,-0.90,-11.50:9.03	0/0:2:-0.00,-0.60,-7.23:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:3:-0.00,-0.90,-11.69:9.03	0/0:2:-0.00,-0.60,-7.42:6.02	0/0:1:-0.00,-0.30,-3.77:3.01	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:1:-0.00,-0.30,-3.77:3.01	0/0:2:-0.00,-0.60,-7.83:6.02	0/0:1:-0.00,-0.30,-3.66:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-11.19:9.03	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.37:3.01	0/0:1:-0.00,-0.30,-3.77:3.01	./.:-1:0,0,0:-1	0/0:5:-0.00,-1.51,-18.62:15.05	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:1:-0.00,-0.30,-3.87:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.92:6.02	0/0:1:-0.00,-0.30,-3.67:3.01	0/0:2:-0.00,-0.60,-7.73:6.02	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-10.98:9.03	0/0:2:-0.00,-0.60,-7.43:6.02
-20	83535	.	G	T	0.01	FDRtranche25.00to35.00+	AB=0.49;AC=6;AF=0.08;AN=98;DB=0;DP=100;Dels=0.00;HRun=1;HaplotypeScore=7.80;MQ=58.27;MQ0=0;OQ=40.35;QD=3.10;SB=-417.00	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-5.96:6.01	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:1:-0.00,-0.30,-3.46:3.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.90:3.00	0/0:2:-0.00,-0.60,-6.40:6.01	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-10.16:9.03	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.26:6.01	0/0:1:-0.01,-0.30,-2.00:2.97	0/0:1:-0.00,-0.30,-3.46:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.37:9.02	0/1:3:-1.60,-0.93,-5.49:6.69	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:1:-0.00,-0.30,-3.06:3.01	0/0:3:-0.02,-0.91,-7.86:8.88	./.:-1:0,0,0:-1	0/1:2:-2.10,-0.61,-3.21:14.86	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:3:-0.00,-0.90,-9.02:9.01	0/0:2:-0.00,-0.60,-5.76:6.01	0/0:2:-0.00,-0.60,-5.90:6.01	0/0:4:-0.01,-1.21,-10.66:11.95	0/0:3:-0.04,-0.92,-6.66:8.77	0/0:1:-0.05,-0.32,-1.20:2.72	0/0:1:-0.01,-0.30,-2.10:2.98	0/0:3:-0.00,-0.91,-9.12:9.02	0/0:2:-0.01,-0.60,-5.40:5.98	0/0:1:-0.00,-0.30,-3.40:3.01	0/0:1:-0.00,-0.30,-3.16:3.01	0/0:3:-0.00,-0.90,-9.87:9.02	1/1:1:-1.69,-0.32,-0.03:2.92	0/0:2:-0.01,-0.61,-5.61:6.00	0/0:3:-0.02,-0.91,-7.82:8.88	0/0:3:-0.04,-0.92,-6.92:8.82	0/0:1:-0.00,-0.30,-2.80:3.00	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.96:3.01	0/0:1:-0.01,-0.31,-1.70:2.92	0/0:4:-0.00,-1.21,-12.07:12.02	0/0:5:-0.01,-1.51,-14.02:14.98	./.:-1:0,0,0:-1	1/1:1:-2.09,-0.31,-0.01:2.97	0/0:2:-0.02,-0.61,-4.86:5.91
-20	83654	.	G	T	0.00	FDRtranche25.00to35.00+	AB=0.70;AC=5;AF=0.06;AN=98;DB=0;DP=118;Dels=0.00;HRun=7;HaplotypeScore=15.30;MQ=57.97;MQ0=0;OQ=22.72;QD=1.89;SB=-437.98	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-6.71:6.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:2:-0.00,-0.60,-6.90:6.02	0/0:5:-0.01,-1.51,-14.47:14.98	0/0:1:-0.00,-0.30,-4.26:3.01	0/0:1:-0.00,-0.30,-2.96:3.01	0/1:3:-1.80,-0.92,-6.04:8.78	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.06:6.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.36:6.01	1/1:1:-3.49,-0.30,-0.00:3.01	0/1:3:-2.10,-0.91,-7.01:11.85	0/0:2:-0.01,-0.61,-5.26:5.97	0/0:1:-0.00,-0.30,-3.16:3.01	0/0:1:-0.00,-0.30,-3.16:3.01	0/0:2:-0.01,-0.61,-5.31:5.98	0/0:2:-0.01,-0.61,-5.61:6.00	0/0:4:-0.01,-1.21,-11.56:12.01	0/0:5:-0.02,-1.51,-13.97:14.96	0/0:1:-0.01,-0.30,-2.36:2.99	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-8.52:8.98	0/0:1:-0.00,-0.30,-2.86:3.00	0/0:3:-0.00,-0.90,-10.02:9.02	0/0:3:-0.00,-0.90,-9.52:9.02	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:4:-0.00,-1.21,-12.77:12.03	0/0:3:-0.00,-0.90,-9.46:9.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:2:-0.00,-0.60,-6.51:6.02	0/0:4:-0.01,-1.21,-11.92:12.00	0/0:4:-0.05,-1.22,-10.77:11.74	0/0:4:-0.00,-1.21,-12.67:12.03	0/0:2:-0.00,-0.60,-6.11:6.01	0/0:2:-0.00,-0.60,-5.76:6.01	0/1:5:-2.23,-1.53,-10.62:7.08	0/0:1:-0.00,-0.30,-2.96:3.01	0/0:2:-0.00,-0.60,-6.46:6.02	0/0:2:-0.00,-0.60,-5.40:6.00	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:4:-0.00,-1.21,-11.97:12.02	0/0:3:-0.00,-0.90,-9.32:9.02	0/0:2:-0.00,-0.60,-6.31:6.01	0/0:1:-0.00,-0.30,-3.00:3.01	./.:-1:0,0,0:-1
-20	83837	.	A	C	0.41	FDRtranche25.00to35.00+	AB=0.67;AC=3;AF=0.03;AN=98;DB=0;DP=150;Dels=0.00;HRun=0;HaplotypeScore=23.77;MQ=57.40;MQ0=0;OQ=14.39;QD=3.60;SB=-460.00	GT:DP:GL:GQ	0/0:2:-0.01,-0.61,-5.73:5.97	0/0:4:-0.04,-1.22,-9.56:11.79	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.43:6.01	1/1:1:-3.26,-0.30,-0.00:3.01	0/0:2:-0.00,-0.60,-6.43:6.01	0/0:1:-0.00,-0.30,-3.24:3.01	0/0:1:-0.00,-0.30,-3.14:3.01	0/0:2:-0.01,-0.60,-4.98:5.99	0/0:4:-2.10,-3.24,-12.96:11.39	0/0:3:-0.01,-0.91,-7.93:8.97	0/0:3:-0.00,-0.90,-9.42:9.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.54:3.01	0/0:3:-0.02,-0.91,-7.87:8.93	0/0:6:-0.01,-1.81,-17.24:17.99	0/0:6:-0.05,-1.83,-17.94:17.78	0/0:2:-0.00,-0.60,-6.63:6.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.58:6.00	0/0:3:-0.00,-0.90,-10.27:9.02	0/0:3:-0.01,-0.91,-7.72:8.99	0/0:3:-0.00,-0.90,-9.52:9.02	0/0:2:-0.00,-0.60,-6.18:6.01	0/0:2:-0.00,-0.60,-5.88:6.01	0/0:4:-0.00,-1.21,-12.71:12.03	0/0:2:-0.01,-0.60,-4.88:5.98	0/0:3:-0.05,-0.92,-6.62:8.72	0/1:3:-2.89,-0.92,-4.68:19.70	0/0:2:-0.00,-0.60,-7.19:6.02	0/0:4:-0.00,-1.21,-12.51:12.02	0/0:3:-0.01,-0.91,-8.82:9.00	0/0:1:-0.00,-0.30,-2.34:2.99	0/0:1:-0.00,-0.30,-3.54:3.01	0/0:4:-0.00,-1.21,-12.61:12.03	0/0:1:-0.00,-0.30,-3.14:3.01	0/0:3:-0.01,-0.91,-9.33:9.00	0/0:1:-0.00,-0.30,-3.34:3.01	0/0:3:-0.01,-0.91,-8.77:8.98	./.:-1:0,0,0:-1	0/0:4:-0.02,-1.21,-11.41:11.90	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.83:6.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.93:6.02	0/0:1:-0.00,-0.30,-3.09:3.01	0/0:5:-0.00,-1.51,-15.79:15.03	0/0:4:-0.01,-1.21,-11.66:12.00	0/0:6:-0.01,-1.81,-18.49:18.03
-20	83940	.	A	G	0.01	FDRtranche25.00to35.00+	AB=0.49;AC=8;AF=0.08;AN=98;DB=0;DP=190;Dels=0.00;HRun=4;HaplotypeScore=51.64;MQ=58.14;MQ0=0;OQ=42.20;QD=3.01;SB=-471.79	GT:DP:GL:GQ	0/0:3:-0.01,-0.91,-10.19:9.01	0/0:6:-0.00,-1.81,-23.26:18.06	1/1:1:-1.70,-0.32,-0.03:2.92	0/0:1:-0.00,-0.30,-4.06:3.01	0/0:4:-0.02,-1.22,-11.65:12.01	0/0:2:-0.00,-0.60,-7.82:6.02	0/0:5:-0.00,-1.51,-17.81:15.04	0/0:1:-0.00,-0.30,-3.96:3.01	0/0:3:-0.00,-0.91,-10.08:9.02	0/0:5:-0.02,-1.52,-16.80:15.02	0/0:5:-0.01,-1.51,-17.31:15.04	0/0:3:-0.01,-0.91,-8.98:9.01	0/0:1:-0.00,-0.30,-2.97:3.01	1/1:1:-1.60,-0.33,-0.04:2.89	0/0:2:-0.00,-0.60,-6.91:6.02	0/0:6:-0.00,-1.81,-21.83:18.06	0/0:6:-0.00,-1.81,-22.56:18.06	0/0:1:-0.00,-0.30,-3.06:3.01	0/0:2:-0.04,-0.63,-5.41:5.94	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:7:-0.01,-2.11,-24.32:21.06	0/0:1:-0.04,-0.33,-1.87:2.95	0/0:5:-0.06,-1.55,-15.31:14.95	0/0:5:-0.00,-1.51,-18.00:15.05	0/0:3:-0.01,-0.91,-9.88:9.01	0/0:10:-0.05,-3.05,-35.61:30.01	0/0:1:-0.00,-0.30,-3.76:3.01	0/0:6:-0.04,-1.84,-20.15:17.99	0/1:3:-1.80,-0.92,-7.43:8.78	0/1:3:-1.50,-0.93,-7.46:5.63	0/0:4:-0.00,-1.21,-15.12:12.04	0/0:3:-0.00,-0.90,-12.08:9.03	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.81:6.02	0/0:3:-0.00,-0.90,-11.08:9.03	0/0:3:-0.00,-0.90,-10.97:9.03	0/0:7:-0.06,-2.16,-21.32:20.96	0/0:1:-0.00,-0.30,-3.86:3.01	0/0:4:-0.02,-1.22,-13.13:12.00	0/1:2:-2.10,-0.61,-2.87:14.87	0/0:3:-0.04,-0.94,-7.88:8.96	0/0:1:-0.00,-0.30,-3.57:3.01	0/0:1:-2.54,-2.61,-2.69:0.71	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.37:3.01	0/1:2:-2.70,-0.60,-3.76:20.92	0/0:7:-0.00,-2.11,-25.81:21.07	0/0:6:-0.03,-1.83,-20.43:17.99	0/0:6:-0.01,-1.81,-20.16:18.04
-20	84036	.	G	A	0.87	FDRtranche25.00to35.00+	AB=0.75;AC=3;AF=0.03;AN=98;DB=0;DP=153;Dels=0.00;HRun=0;HaplotypeScore=17.30;MQ=57.20;MQ0=0;OQ=14.23;QD=2.85;SB=-487.46	GT:DP:GL:GQ	0/0:3:-0.00,-0.91,-9.36:9.02	0/0:3:-0.00,-0.90,-9.93:9.02	0/0:5:-0.00,-1.51,-17.23:15.04	0/1:4:-4.07,-1.21,-9.53:28.64	0/0:6:-0.01,-1.82,-17.54:18.01	0/0:3:-0.01,-0.91,-9.03:9.00	0/0:3:-0.00,-0.90,-9.43:9.02	0/0:7:-0.01,-2.11,-21.89:21.04	0/0:2:-0.00,-0.60,-5.99:6.01	0/0:8:-0.04,-2.43,-21.10:23.89	0/0:3:-0.00,-0.90,-10.36:9.03	0/0:6:-0.02,-1.82,-17.37:17.99	1/1:1:-2.36,-0.31,-0.01:2.99	0/0:2:-0.00,-0.60,-6.76:6.02	0/0:1:-0.00,-0.30,-2.87:3.00	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.44:6.02	0/0:1:-0.00,-0.30,-2.50:3.00	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:2:-0.00,-0.60,-5.64:6.01	0/0:7:-0.01,-2.11,-21.52:21.04	0/0:4:-0.00,-1.21,-12.33:12.02	0/0:1:-0.00,-0.30,-3.37:3.01	0/0:3:-0.01,-0.91,-8.86:9.01	0/0:7:-0.02,-2.12,-20.23:21.01	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:1:-0.01,-0.31,-1.77:2.93	0/0:5:-0.01,-1.51,-14.50:15.02	0/0:3:-0.00,-0.90,-10.13:9.03	0/0:3:-0.00,-0.90,-9.13:9.02	0/0:2:-0.01,-0.61,-5.06:5.94	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:1:-0.00,-0.30,-3.00:3.01	0/0:2:-0.01,-0.61,-5.49:5.97	0/0:2:-0.04,-0.62,-3.66:5.84	0/0:2:-0.02,-0.61,-4.64:5.92	0/0:3:-0.01,-0.91,-8.73:9.01	0/0:4:-0.05,-1.24,-10.93:11.88	./.:-1:0,0,0:-1	0/0:3:-0.03,-0.91,-7.11:8.89	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.76:6.02	0/0:2:-0.00,-0.60,-6.34:6.01	0/0:4:-0.00,-1.21,-12.43:12.03	0/0:2:-0.00,-0.60,-6.86:6.02	0/0:6:-0.07,-1.85,-15.22:17.83	0/0:4:-0.04,-1.23,-10.80:11.91
-20	84430	.	C	A	0.86	FDRtranche25.00to35.00+	AB=0.59;AC=2;AF=0.02;AN=98;DB=0;DP=206;Dels=0.00;HRun=0;HaplotypeScore=44.08;MQ=57.23;MQ0=0;OQ=19.65;QD=3.93;SB=-490.98	GT:DP:GL:GQ	0/0:2:-0.01,-0.60,-4.70:5.98	0/0:7:-0.03,-2.12,-18.17:20.96	0/0:1:-0.00,-0.30,-2.70:3.00	0/0:1:-0.00,-0.30,-2.20:2.98	0/0:6:-0.02,-1.82,-16.53:17.95	0/0:3:-0.00,-0.91,-8.72:9.01	0/0:8:-0.02,-2.42,-22.13:23.98	0/0:11:-0.07,-3.34,-27.48:32.67	0/0:4:-0.00,-1.21,-12.42:12.02	0/0:6:-0.03,-1.82,-15.66:17.85	0/0:5:-0.01,-1.51,-13.82:14.98	0/0:1:-0.00,-0.30,-2.60:3.00	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.40:6.00	0/0:2:-0.00,-0.60,-5.40:6.00	0/0:5:-0.01,-1.51,-14.57:15.01	0/0:6:-0.01,-1.81,-19.09:18.04	0/0:1:-0.00,-0.30,-2.50:3.00	0/0:2:-0.01,-0.60,-4.70:5.98	0/1:2:-3.60,-0.60,-3.06:24.55	0/0:4:-0.01,-1.21,-11.26:12.00	0/0:9:-0.02,-2.72,-26.25:27.00	0/0:6:-0.01,-1.81,-17.12:18.01	0/0:3:-0.00,-0.90,-9.16:9.02	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:4:-0.01,-1.21,-11.46:12.00	0/0:5:-0.02,-1.51,-12.40:14.94	0/0:7:-0.01,-2.11,-18.97:20.99	0/0:5:-0.01,-1.51,-12.92:14.98	0/0:2:-0.00,-0.60,-5.16:6.00	0/0:4:-0.01,-1.21,-10.92:12.00	0/0:6:-0.01,-1.81,-17.32:18.01	0/0:1:-0.00,-0.30,-2.40:2.99	0/0:2:-0.00,-0.60,-6.06:6.01	0/0:2:-0.00,-0.60,-5.86:6.00	0/0:2:-0.00,-0.60,-5.10:6.00	0/0:2:-0.00,-0.60,-5.46:6.00	0/0:4:-0.01,-1.21,-10.06:11.99	0/0:3:-0.00,-0.91,-8.72:9.01	0/0:2:-0.00,-0.60,-5.20:6.00	0/0:2:-0.00,-0.60,-5.66:6.00	0/0:3:-0.01,-0.91,-7.72:8.98	0/0:2:-0.01,-0.60,-4.60:5.98	0/0:2:-0.00,-0.60,-7.11:6.02	0/0:5:-0.01,-1.51,-14.93:15.01	0/0:7:-0.03,-2.12,-18.99:20.96	0/0:12:-0.02,-3.62,-34.10:36.01	0/0:9:-0.02,-2.72,-25.93:26.98	0/1:3:-3.70,-0.90,-6.71:27.92
-20	84788	.	C	A	0.00	FDRtranche25.00to35.00+	AB=0.55;AC=5;AF=0.05;AN=98;DB=0;DP=184;Dels=0.00;HRun=4;HaplotypeScore=24.13;MQ=56.57;MQ0=0;OQ=15.51;QD=0.97;SB=-470.98	GT:DP:GL:GQ	0/0:3:-0.00,-0.90,-10.17:9.03	0/0:7:-0.04,-2.12,-20.24:20.82	0/0:3:-0.02,-0.91,-8.56:8.92	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:4:-0.01,-1.21,-11.92:12.01	0/0:5:-0.00,-1.51,-16.77:15.04	0/0:6:-0.01,-1.81,-19.59:18.03	0/0:5:-0.01,-1.51,-14.97:15.01	0/0:7:-0.01,-2.11,-23.44:21.05	0/0:2:-0.00,-0.60,-6.81:6.02	0/0:5:-0.01,-1.51,-16.03:15.03	0/0:3:-0.01,-0.91,-9.07:9.01	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-11.96:12.01	0/0:4:-0.05,-1.22,-10.97:11.74	0/0:4:-0.00,-1.21,-12.97:12.03	0/0:2:-0.00,-0.60,-6.71:6.02	0/0:3:-0.00,-0.90,-9.26:9.02	1/1:1:-2.29,-0.31,-0.01:2.99	0/0:2:-0.01,-0.60,-4.90:5.97	0/0:4:-0.03,-1.22,-10.87:11.95	0/0:6:-0.05,-1.84,-16.23:17.87	0/0:6:-0.01,-1.81,-18.03:18.00	0/0:1:-0.00,-0.30,-3.46:3.01	0/1:2:-2.60,-0.60,-3.30:19.91	0/0:5:-0.01,-1.51,-15.37:15.02	0/0:4:-0.00,-1.21,-13.13:12.03	0/1:4:-2.20,-1.21,-9.91:9.85	0/0:3:-0.01,-0.91,-8.16:8.98	0/0:2:-0.00,-0.60,-5.36:6.00	0/0:2:-0.00,-0.60,-5.81:6.01	0/0:4:-0.01,-1.21,-12.02:11.97	0/0:3:-0.06,-0.92,-5.60:8.67	./.:-1:0,0,0:-1	0/0:4:-0.04,-1.22,-10.56:11.80	0/0:4:-0.00,-1.21,-13.53:12.03	0/0:3:-0.00,-0.90,-9.37:9.02	0/1:6:-2.00,-1.82,-15.19:1.82	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-9.02:9.01	0/0:2:-0.00,-0.60,-6.61:6.02	./.:-1:0,0,0:-1	0/0:3:-0.03,-0.91,-7.82:8.85	0/0:1:-0.00,-0.30,-3.06:3.01	0/0:2:-0.00,-0.60,-6.36:6.01	0/0:3:-0.00,-0.90,-9.47:9.02	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:2:-0.00,-0.60,-6.81:6.02	0/0:3:-0.00,-0.90,-9.96:9.02
-20	85189	.	A	G	1.97	FDRtranche12.50to25.00	AB=0.50;AC=3;AF=0.03;AN=98;DB=0;DP=146;Dels=0.00;HRun=1;HaplotypeScore=17.84;MQ=57.69;MQ0=0;OQ=16.61;QD=5.54;SB=-514.67	GT:DP:GL:GQ	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-4.07:3.01	0/0:3:-0.00,-0.90,-11.28:9.03	0/0:3:-0.00,-0.91,-10.40:9.03	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:3:-0.04,-0.94,-8.18:8.95	1/1:1:-3.00,-0.30,-0.00:3.01	0/0:3:-0.00,-0.90,-11.48:9.03	0/0:3:-0.00,-0.90,-11.38:9.03	0/1:2:-3.07,-0.60,-3.96:24.66	0/0:2:-0.00,-0.60,-7.72:6.02	0/0:1:-0.03,-0.32,-1.97:2.96	./.:-1:0,0,0:-1	0/0:6:-0.00,-1.81,-23.35:18.06	0/0:4:-0.01,-1.21,-14.75:12.03	0/0:2:-0.00,-0.60,-7.72:6.02	0/0:2:-0.00,-0.60,-8.01:6.02	0/0:3:-0.00,-0.90,-10.69:9.03	0/0:1:-0.00,-0.30,-3.67:3.01	0/0:5:-0.00,-1.51,-18.01:15.05	0/0:1:-0.02,-0.32,-2.17:2.98	0/0:5:-0.01,-1.52,-17.00:15.02	0/0:1:-0.00,-0.30,-3.76:3.01	0/0:2:-0.00,-0.60,-7.72:6.02	0/0:1:-0.01,-0.31,-2.57:3.00	0/0:3:-0.00,-0.91,-10.78:9.03	0/0:5:-0.01,-1.51,-17.89:15.04	0/0:4:-0.00,-1.21,-14.36:12.04	0/0:8:-0.00,-2.41,-29.66:24.07	0/0:1:-0.00,-0.30,-3.86:3.01	0/0:3:-0.01,-0.91,-10.19:9.02	0/0:4:-0.00,-1.20,-16.03:12.04	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:3:-0.00,-0.90,-11.79:9.03	0/0:2:-0.00,-0.60,-7.71:6.02	0/0:2:-0.00,-0.60,-7.03:6.02	0/0:1:-0.00,-0.30,-3.47:3.01	0/0:4:-0.00,-1.21,-15.15:12.04	0/0:4:-0.00,-1.21,-14.05:12.03	0/0:3:-0.00,-0.91,-10.58:9.02	0/0:5:-0.04,-1.54,-16.92:14.98	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:3:-0.00,-0.90,-11.18:9.03	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:2:-0.00,-0.60,-6.62:6.02	0/0:2:-0.00,-0.60,-7.72:6.02	0/0:5:-0.00,-1.51,-18.09:15.04	0/0:6:-0.01,-1.81,-19.79:18.04
-20	85439	.	C	A	0.00	FDRtranche25.00to35.00+	AB=0.62;AC=3;AF=0.04;AN=98;DB=0;DP=163;Dels=0.00;HRun=4;HaplotypeScore=28.48;MQ=55.14;MQ0=0;OQ=22.61;QD=1.19;SB=-442.95	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-5.86:6.00	0/0:4:-0.00,-1.21,-13.02:12.02	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.87:9.02	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:1:-0.00,-0.30,-2.30:2.99	0/0:3:-0.00,-0.91,-9.37:9.02	0/0:2:-0.00,-0.60,-6.86:6.02	0/0:3:-0.00,-0.90,-9.92:9.02	0/0:1:-0.00,-0.30,-3.06:3.01	0/0:2:-0.00,-0.60,-6.61:6.02	0/0:3:-0.00,-0.90,-10.17:9.03	0/1:3:-2.10,-0.91,-6.77:11.85	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:5:-0.00,-1.51,-16.03:15.04	./.:-1:0,0,0:-1	0/0:6:-0.00,-1.81,-19.64:18.05	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:2:-0.06,-0.63,-3.06:5.75	0/0:2:-0.00,-0.60,-6.61:6.02	0/0:3:-0.00,-0.90,-9.82:9.02	0/0:4:-0.00,-1.21,-12.43:12.03	0/0:8:-0.02,-2.42,-23.70:23.95	0/0:3:-0.00,-0.90,-9.47:9.02	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:2:-0.00,-0.60,-6.41:6.02	0/0:2:-0.02,-0.61,-4.80:5.88	0/0:5:-0.02,-1.51,-14.73:14.95	0/0:2:-0.00,-0.60,-7.01:6.02	0/0:3:-0.00,-0.90,-9.97:9.02	0/0:4:-0.00,-1.21,-13.87:12.04	0/0:2:-0.00,-0.60,-5.96:6.01	0/0:1:-0.00,-0.30,-2.90:3.00	0/0:5:-0.00,-1.51,-15.77:15.03	0/0:4:-0.01,-1.21,-11.83:12.02	0/0:7:-0.02,-2.12,-20.34:21.00	0/0:6:-1.60,-1.83,-15.97:2.34	0/0:2:-0.00,-0.60,-5.56:6.00	0/0:1:-0.00,-0.30,-3.26:3.01	0/1:6:-2.60,-1.81,-14.49:7.89	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:2:-0.00,-0.60,-5.40:6.00	0/0:3:-0.00,-0.90,-9.47:9.02	0/0:3:-0.00,-0.90,-9.77:9.02	0/0:2:-0.03,-0.61,-4.66:5.84	0/1:5:-3.60,-1.51,-13.07:20.91
-20	85878	.	C	A	0.01	FDRtranche25.00to35.00+	AB=0.63;AC=4;AF=0.05;AN=98;DB=0;DP=126;Dels=0.00;HRun=3;HaplotypeScore=10.08;MQ=55.13;MQ0=0;OQ=12.67;QD=1.81;SB=-420.98	GT:DP:GL:GQ	0/0:4:-0.00,-1.20,-13.76:12.03	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:3:-0.00,-0.90,-9.72:9.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.60:6.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.81:6.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.86:6.02	0/0:3:-0.00,-0.90,-9.42:9.02	0/0:2:-0.00,-0.60,-6.56:6.02	0/0:3:-0.00,-0.90,-9.56:9.02	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:1:-0.00,-0.30,-3.00:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.06:6.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.86:3.00	0/1:4:-2.60,-1.21,-9.17:13.90	0/0:4:-0.00,-1.21,-12.93:12.03	0/0:2:-0.00,-0.60,-5.66:6.00	0/0:2:-0.00,-0.60,-6.31:6.01	0/0:5:-0.01,-1.51,-14.16:14.99	0/0:5:-0.01,-1.51,-14.12:15.00	0/0:5:-0.01,-1.51,-14.72:14.97	0/0:4:-0.00,-1.21,-12.63:12.03	0/0:2:-0.00,-0.60,-5.56:6.00	0/0:4:-0.01,-1.21,-11.50:11.96	0/1:2:-1.90,-0.61,-2.42:12.83	./.:-1:0,0,0:-1	0/0:5:-0.01,-1.51,-15.37:14.99	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-8.86:9.01	1/1:1:-2.49,-0.30,-0.00:3.00	0/0:2:-0.00,-0.60,-5.80:6.01	0/0:3:-0.01,-0.91,-7.96:8.99	0/0:3:-0.00,-0.91,-9.27:9.02	0/0:2:-0.00,-0.60,-6.51:6.02	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:2:-0.00,-0.60,-5.96:6.01	0/0:2:-0.00,-0.60,-6.96:6.02	0/0:2:-0.00,-0.60,-6.00:6.01	0/0:5:-0.01,-1.51,-13.46:15.00	0/0:2:-0.00,-0.60,-6.16:6.01	0/0:2:-0.00,-0.60,-6.76:6.02	0/0:3:-0.00,-0.90,-9.92:9.02
-20	85990	.	G	A	0.01	FDRtranche25.00to35.00+	AB=0.78;AC=3;AF=0.03;AN=98;DB=0;DP=129;Dels=0.00;HRun=4;HaplotypeScore=34.82;MQ=54.61;MQ0=0;OQ=23.05;QD=1.65;SB=-431.97	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-7.29:6.02	0/0:1:-0.00,-0.30,-3.40:3.01	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:2:-0.00,-0.60,-7.19:6.02	0/0:6:-0.02,-1.82,-15.64:17.95	0/0:2:-0.01,-0.61,-5.46:5.96	0/0:1:-0.01,-0.30,-2.07:2.97	0/0:3:-0.00,-0.90,-10.49:9.03	0/0:1:-0.00,-0.30,-3.47:3.01	0/0:2:-0.00,-0.60,-6.99:6.02	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.40:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.89:6.02	0/0:2:-0.00,-0.60,-6.46:6.02	0/0:1:-0.00,-0.30,-3.40:3.01	0/0:5:-0.01,-1.51,-15.43:14.98	0/0:2:-0.00,-0.60,-6.06:6.01	0/0:2:-0.00,-0.60,-6.34:6.01	0/0:2:-0.00,-0.60,-6.24:6.01	0/0:4:-0.01,-1.21,-12.68:12.02	0/0:2:-0.00,-0.60,-5.86:6.00	0/0:1:-0.00,-0.30,-3.60:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.99:6.02	0/0:5:-0.02,-1.51,-15.25:14.95	0/0:3:-0.00,-0.91,-9.16:9.01	./.:-1:0,0,0:-1	0/0:2:-0.01,-0.61,-4.14:5.95	0/0:1:-0.00,-0.30,-3.60:3.01	0/0:2:-0.00,-0.60,-6.46:6.01	0/0:4:-0.00,-1.21,-12.63:12.03	0/0:3:-0.01,-0.91,-8.86:9.00	0/0:1:-0.00,-0.30,-3.50:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.69:6.02	0/0:3:-0.01,-0.91,-7.81:8.98	0/0:4:-0.03,-1.22,-11.53:11.88	0/0:4:-0.01,-1.21,-12.68:12.02	0/1:4:-3.56,-1.21,-9.29:23.53	0/0:2:-0.00,-0.60,-6.04:6.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.44:6.00	0/0:3:-0.00,-0.90,-10.06:9.02	0/1:4:-2.66,-1.21,-8.64:14.50	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:2:-0.00,-0.60,-6.24:6.01	0/1:4:-3.66,-1.21,-9.46:24.53
-20	85993	.	C	A	0.05	FDRtranche25.00to35.00+	AB=0.60;AC=4;AF=0.04;AN=98;DB=0;DP=128;Dels=0.00;HRun=2;HaplotypeScore=31.32;MQ=53.70;MQ0=0;OQ=28.43;QD=3.16;SB=-447.96	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-6.91:6.02	0/0:1:-0.00,-0.30,-3.56:3.01	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:2:-0.00,-0.60,-6.51:6.02	0/0:7:-0.05,-2.13,-20.06:20.76	0/0:2:-0.00,-0.60,-6.36:6.01	0/0:1:-0.00,-0.30,-2.70:3.00	0/0:3:-0.00,-0.90,-9.67:9.02	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:2:-0.00,-0.60,-6.81:6.02	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.21:6.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:2:-0.00,-0.60,-5.56:6.00	0/0:1:-0.00,-0.30,-3.06:3.01	0/0:5:-0.01,-1.51,-14.97:15.02	0/0:1:-0.00,-0.30,-3.10:3.01	0/0:2:-0.00,-0.60,-6.10:6.01	0/0:3:-0.01,-0.91,-8.20:8.97	0/0:4:-0.00,-1.21,-12.73:12.03	0/0:4:-0.05,-1.22,-10.46:11.74	0/0:1:-0.00,-0.30,-3.06:3.01	1/1:1:-2.39,-0.30,-0.01:2.99	0/0:2:-0.00,-0.60,-5.91:6.01	0/0:5:-0.02,-1.51,-13.63:14.97	0/0:3:-0.00,-0.90,-9.62:9.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:2:-0.00,-0.60,-6.61:6.02	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:3:-0.00,-0.90,-9.56:9.02	0/0:3:-0.00,-0.90,-10.02:9.02	0/0:2:-0.00,-0.60,-6.71:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.11:6.01	0/0:3:-0.00,-0.90,-9.80:9.02	0/0:3:-0.00,-0.90,-9.42:9.02	0/0:4:-0.01,-1.21,-11.73:12.02	0/1:4:-2.70,-1.21,-9.77:14.90	0/0:2:-0.00,-0.60,-6.30:6.01	./.:-1:0,0,0:-1	0/0:2:-0.01,-0.61,-5.20:5.93	0/0:3:-0.00,-0.90,-9.52:9.02	0/0:2:-0.00,-0.60,-5.66:6.01	0/0:2:-0.04,-0.62,-4.56:5.79	0/0:3:-0.00,-0.90,-9.10:9.02	0/1:2:-3.50,-0.60,-2.76:21.54
-20	86005	.	C	A	196.75	InDel	AB=0.54;AC=8;AF=0.10;AN=98;DB=0;DP=120;Dels=0.04;HRun=17;HaplotypeScore=43.84;MQ=51.77;MQ0=0;QD=5.47;SB=-392.24	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-6.91:6.02	0/0:2:-0.00,-0.60,-6.91:6.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:3:-0.00,-0.90,-9.30:9.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:3:-0.01,-0.91,-8.62:8.99	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.71:6.02	./.:-1:0,0,0:-1	0/0:1:-0.04,-0.31,-1.30:2.78	0/0:1:-0.00,-0.30,-3.26:3.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:1:-0.00,-0.30,-2.76:3.00	./.:-1:0,0,0:-1	0/1:8:-2.75,-2.41,-20.89:3.33	0/0:1:-0.00,-0.30,-3.16:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-8.86:9.01	0/1:6:-3.10,-1.81,-15.79:12.89	0/0:2:-0.00,-0.30,-3.16:3.01	0/0:2:-0.00,-0.60,-6.61:6.02	0/1:3:-2.80,-0.91,-6.42:18.91	0/1:4:-3.01,-1.21,-7.52:17.94	0/0:7:-0.01,-2.11,-21.99:21.05	0/0:3:-0.00,-0.91,-9.17:9.02	0/0:2:-0.00,-0.60,-6.61:6.02	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:1:-0.00,-0.30,-3.36:3.01	0/1:3:-4.56,-2.28,-4.66:22.84	0/0:3:-0.02,-0.91,-8.16:8.88	0/1:2:-3.10,-0.60,-3.26:24.92	0/1:6:-9.69,-1.51,-6.62:51.09	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:2:-0.03,-0.62,-4.71:5.92	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:2:-0.00,-0.60,-6.11:6.01	0/0:5:-0.01,-1.51,-14.19:15.01	0/0:3:-0.00,-0.60,-6.51:6.02	0/1:2:-3.60,-0.60,-3.30:26.99	0/0:1:-0.00,-0.30,-2.56:3.00	0/0:2:-0.01,-0.60,-5.00:5.97	0/0:4:-0.01,-1.21,-11.67:12.01	0/0:3:-0.03,-0.91,-7.66:8.84	0/0:2:-0.01,-0.60,-5.36:5.99	0/0:1:-0.00,-0.30,-3.00:3.01	0/0:4:-0.00,-0.60,-5.30:6.00
-20	86023	.	C	A	-0.00	FDRtranche25.00to35.00+	AB=0.70;AC=7;AF=0.08;AN=98;DB=0;DP=177;Dels=0.03;HRun=17;HaplotypeScore=114.74;MQ=52.27;MQ0=0;OQ=121.54;QD=5.06;SB=-479.18	GT:DP:GL:GQ	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:3:-0.02,-0.92,-8.42:8.95	0/0:2:-0.00,-0.60,-5.96:6.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.06:6.01	0/0:1:-0.00,-0.30,-2.60:3.00	0/0:2:-0.00,-0.60,-6.71:6.02	0/0:3:-0.00,-0.90,-9.92:9.02	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:2:-0.01,-0.61,-5.41:5.97	0/0:2:-0.00,-0.60,-5.66:6.00	0/0:2:-0.01,-0.61,-5.10:5.93	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:2:-0.00,-0.60,-5.96:6.01	0/0:2:-0.00,-0.60,-6.86:6.02	0/0:3:-0.03,-0.92,-7.17:8.94	0/0:2:-0.01,-0.61,-5.56:5.98	0/0:4:-0.03,-1.22,-9.87:11.93	0/0:4:-0.01,-1.21,-11.37:12.00	0/0:2:-0.00,-0.60,-6.50:6.02	0/0:3:-0.00,-0.90,-9.60:9.02	0/1:7:-5.35,-2.15,-11.62:32.03	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:7:-0.01,-1.81,-17.53:18.02	0/0:4:-0.00,-1.21,-12.62:12.03	0/1:6:-3.24,-1.81,-15.67:14.34	0/0:5:-0.00,-1.21,-12.86:12.03	0/0:1:-0.00,-0.30,-2.56:3.00	0/0:2:-0.01,-0.61,-4.86:5.97	0/0:2:-0.01,-0.61,-4.10:5.94	0/0:5:-0.00,-1.51,-15.56:15.03	0/0:3:-0.00,-0.90,-10.26:9.03	0/0:4:-0.00,-1.21,-12.66:12.03	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:6:-0.00,-1.51,-15.96:15.04	0/0:4:-0.01,-1.21,-11.17:12.00	1/1:1:-2.94,-0.30,-0.00:3.01	0/1:2:-2.54,-0.60,-3.26:19.36	0/0:5:-1.39,-1.55,-10.61:1.63	0/0:4:-0.08,-1.25,-8.93:11.76	0/0:4:-0.01,-1.21,-11.52:11.99	0/0:2:-0.00,-0.60,-5.80:6.01	0/0:6:-0.06,-1.83,-15.63:17.73	0/0:1:-0.00,-0.30,-3.26:3.01	1/1:2:-4.68,-0.61,-0.01:5.93	0/0:2:-0.00,-0.60,-6.51:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:6:-0.00,-1.81,-19.37:18.05
-20	86025	.	T	A	0.06	FDRtranche25.00to35.00+	AB=0.80;AC=7;AF=0.08;AN=98;DB=0;DP=174;Dels=0.01;HRun=1;HaplotypeScore=77.92;MQ=53.20;MQ0=0;OQ=85.41;QD=2.31;SB=-447.05	GT:DP:GL:GQ	0/0:1:-0.00,-0.30,-3.44:3.01	0/0:2:-0.00,-0.60,-7.24:6.02	0/0:2:-0.01,-0.61,-5.74:6.00	0/0:1:-0.01,-0.31,-2.04:2.97	0/0:2:-0.00,-0.60,-6.74:6.02	0/0:1:-0.01,-0.31,-2.10:2.97	0/0:2:-0.00,-0.60,-7.18:6.02	0/0:4:-0.01,-1.21,-12.28:12.02	0/0:1:-0.00,-0.30,-3.44:3.01	0/0:3:-0.03,-0.92,-7.22:8.91	0/0:2:-0.01,-0.61,-5.84:6.00	0/0:1:-0.00,-0.30,-3.50:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.14:6.02	0/0:2:-0.00,-0.60,-6.14:6.01	0/0:2:-0.00,-0.60,-5.88:6.01	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:3:-0.01,-0.91,-8.48:9.00	0/0:5:-0.07,-1.54,-12.06:14.78	0/0:2:-0.00,-0.60,-6.90:6.02	0/1:5:-2.01,-1.53,-11.19:4.84	0/1:5:-3.52,-1.52,-11.24:20.02	0/0:2:-0.03,-0.62,-4.74:5.94	0/0:6:-1.70,-1.83,-16.95:1.33	0/0:4:-0.02,-1.22,-12.38:11.98	0/0:3:-0.00,-0.90,-10.14:9.03	0/1:5:-2.10,-1.52,-13.35:5.84	./.:-1:0,0,0:-1	0/1:2:-1.64,-0.67,-1.64:9.75	0/0:2:-0.00,-0.60,-6.50:6.02	0/0:3:-0.00,-0.91,-9.90:9.02	0/0:3:-0.00,-0.90,-10.84:9.03	0/0:4:-0.00,-1.21,-13.13:12.03	0/0:1:-0.04,-0.33,-1.70:2.92	0/0:6:-0.00,-1.51,-16.73:15.04	0/0:4:-0.05,-1.24,-9.82:11.88	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.34:3.01	0/0:4:-0.00,-0.90,-10.18:9.03	0/1:2:-3.70,-0.60,-3.34:27.37	0/0:2:-0.00,-0.60,-6.74:6.02	0/0:2:-0.00,-0.60,-6.70:6.02	0/0:4:-0.00,-1.21,-12.32:12.02	0/0:1:-0.00,-0.30,-3.44:3.01	1/1:2:-5.20,-0.62,-0.02:5.97	0/0:3:-0.00,-0.90,-10.02:9.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.74:6.02	0/0:6:-0.00,-1.81,-20.51:18.05
-20	86037	.	T	A	0.00	FDRtranche25.00to35.00+	AB=0.69;AC=3;AF=0.04;AN=98;DB=0;DP=217;Dels=0.00;HRun=3;HaplotypeScore=46.21;MQ=56.30;MQ0=0;OQ=11.84;QD=0.62;SB=-477.48	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-6.98:6.02	0/0:4:-0.00,-1.21,-14.02:12.04	0/0:2:-0.00,-0.60,-7.14:6.02	./.:-1:0,0,0:-1	0/1:4:-2.44,-1.21,-10.08:12.34	0/0:2:-0.01,-0.61,-5.64:6.00	0/0:3:-0.00,-0.90,-11.02:9.03	0/0:5:-0.00,-1.51,-17.91:15.05	0/0:1:-0.00,-0.30,-3.54:3.01	0/0:4:-0.01,-1.21,-11.96:12.02	0/0:1:-0.00,-0.30,-3.64:3.01	0/1:2:-2.50,-0.61,-3.34:18.93	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-12.62:12.02	0/0:2:-0.00,-0.60,-6.64:6.02	0/0:6:-0.03,-1.82,-17.59:17.93	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:2:-0.00,-0.60,-6.14:6.01	0/1:5:-3.10,-1.51,-13.12:15.93	0/0:2:-0.00,-0.60,-6.34:6.01	0/0:5:-0.00,-1.51,-16.71:15.03	0/0:9:-2.15,-2.75,-22.56:6.07	0/0:2:-0.00,-0.60,-6.38:6.01	0/0:9:-0.02,-2.72,-28.43:26.99	0/0:3:-0.00,-0.90,-10.08:9.02	0/0:7:-0.01,-2.11,-23.13:21.05	0/0:4:-0.05,-1.24,-10.58:11.91	0/0:1:-0.00,-0.30,-2.60:3.00	0/0:3:-0.05,-0.94,-7.24:8.90	0/0:2:-0.00,-0.60,-6.40:6.01	0/0:3:-0.00,-0.90,-10.18:9.03	0/0:5:-0.01,-1.51,-16.11:15.01	0/0:5:-0.01,-1.51,-15.31:15.02	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:5:-0.00,-1.51,-17.11:15.04	0/0:6:-0.02,-1.82,-16.39:17.96	./.:-1:0,0,0:-1	0/0:5:-0.00,-1.51,-17.20:15.04	0/0:7:-0.05,-2.14,-19.75:20.90	0/0:6:-0.00,-1.81,-19.29:18.04	0/0:6:-0.00,-1.81,-19.63:18.04	0/0:2:-0.00,-0.60,-6.60:6.02	0/0:7:-0.02,-2.12,-20.89:21.02	0/0:2:-0.00,-0.60,-7.18:6.02	./.:-1:0,0,0:-1	0/0:6:-0.00,-1.81,-19.93:18.05	0/0:2:-0.00,-0.60,-6.74:6.02	0/0:3:-0.00,-0.90,-9.98:9.02	0/0:6:-0.00,-1.81,-20.29:18.05
-20	86792	.	C	A	0.34	FDRtranche25.00to35.00+	AB=0.67;AC=1;AF=0.01;AN=98;DB=0;DP=168;Dels=0.00;HRun=2;HaplotypeScore=10.70;MQ=56.94;MQ0=0;OQ=16.67;QD=2.78;SB=-530.35	GT:DP:GL:GQ	0/0:3:-0.00,-0.90,-9.56:9.02	0/0:2:-0.02,-0.61,-4.70:5.91	0/0:1:-0.00,-0.30,-3.56:3.01	0/0:3:-0.00,-0.90,-9.97:9.02	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:4:-0.00,-1.20,-13.66:12.03	0/0:5:-0.03,-1.52,-15.47:14.94	0/0:5:-0.00,-1.51,-17.43:15.04	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:4:-0.00,-1.21,-14.13:12.04	0/0:3:-0.00,-0.90,-8.86:9.01	0/0:2:-0.00,-0.60,-5.56:6.00	0/0:3:-0.01,-0.91,-9.57:9.00	0/0:3:-0.02,-0.91,-7.80:8.93	0/0:3:-0.00,-0.90,-10.12:9.02	0/0:3:-0.00,-0.90,-10.52:9.03	0/0:2:-0.00,-0.60,-6.31:6.01	0/0:2:-0.00,-0.60,-6.10:6.01	0/1:6:-7.04,-1.81,-12.47:52.30	0/0:2:-0.00,-0.60,-7.00:6.02	0/0:4:-0.00,-1.21,-12.77:12.03	0/0:3:-0.00,-0.90,-9.52:9.02	0/0:5:-0.00,-1.51,-16.49:15.04	0/0:2:-0.00,-0.60,-6.56:6.02	0/0:3:-0.00,-0.90,-9.62:9.02	0/0:1:-0.00,-0.30,-2.20:2.98	0/0:3:-0.00,-0.90,-8.76:9.00	0/0:1:-0.00,-0.30,-3.56:3.01	0/0:5:-0.01,-1.51,-14.22:15.01	0/0:3:-0.01,-0.91,-8.82:9.01	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:2:-0.00,-0.60,-6.71:6.02	0/0:8:-0.03,-2.42,-24.64:23.92	0/0:4:-0.00,-1.21,-12.66:12.02	0/0:1:-0.01,-0.30,-2.00:2.97	0/0:2:-0.00,-0.60,-5.56:6.00	0/0:2:-0.00,-0.60,-6.30:6.01	0/0:7:-0.02,-2.12,-21.23:20.99	0/0:6:-0.00,-1.81,-19.02:18.04	0/0:1:-0.00,-0.30,-3.10:3.01	0/0:5:-0.00,-1.51,-15.87:15.04	./.:-1:0,0,0:-1	0/0:4:-0.01,-1.21,-11.46:12.01	0/0:4:-0.01,-1.21,-12.12:12.02	0/0:4:-0.00,-1.21,-12.82:12.03	0/0:4:-0.00,-1.21,-13.47:12.03	0/0:6:-0.01,-1.81,-19.22:18.04
-20	87112	rs34383360	G	A	60.64	0	AB=0.54;AC=33;AF=0.41;AN=98;DB=1;DP=131;Dels=0.00;HRun=3;HaplotypeScore=7.75;MQ=57.62;MQ0=0;OQ=1955.68;QD=23.85;SB=-1255.68	GT:DP:GL:GQ	0/1:3:-7.42,-0.91,-2.80:18.92	1/1:3:-11.48,-0.90,-0.00:9.03	0/0:2:-0.01,-0.61,-5.76:6.00	0/0:1:-0.00,-0.30,-3.17:3.01	1/1:3:-10.68,-0.90,-0.00:9.03	0/0:1:-0.00,-0.30,-2.80:3.00	./.:-1:0,0,0:-1	0/1:3:-7.24,-0.91,-3.00:20.92	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.61,-5.59:6.01	0/1:5:-6.94,-1.51,-8.39:54.29	0/1:2:-3.87,-0.60,-2.80:21.93	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.74:6.02	0/0:1:-0.00,-0.30,-3.27:3.01	1/1:1:-3.66,-0.30,-0.00:3.01	0/0:1:-0.00,-0.30,-3.17:3.01	1/1:6:-21.18,-1.82,-0.01:18.04	0/0:2:-0.01,-0.61,-5.39:5.99	1/1:3:-11.29,-0.90,-0.00:9.03	0/1:5:-7.73,-1.51,-8.59:62.19	0/0:5:-0.02,-1.52,-12.83:14.97	0/0:1:-0.00,-0.30,-2.80:3.00	0/0:7:-0.01,-2.12,-20.63:21.02	0/0:4:-0.03,-1.23,-10.28:11.93	0/1:4:-11.38,-1.21,-2.70:14.90	1/1:5:-18.20,-1.51,-0.00:15.05	0/0:3:-0.01,-0.91,-7.76:8.98	0/0:1:-0.00,-0.30,-3.00:3.01	0/1:6:-14.64,-1.81,-5.87:40.57	1/1:4:-14.95,-1.21,-0.00:12.04	0/0:3:-0.01,-0.91,-8.03:8.98	1/1:2:-6.73,-0.61,-0.01:6.01	0/0:5:-0.01,-1.51,-14.63:15.03	0/1:4:-3.91,-1.23,-5.86:26.81	0/0:1:-0.00,-0.30,-2.80:3.00	./.:-1:0,0,0:-1	0/1:3:-3.87,-0.91,-5.76:29.65	0/0:2:-0.00,-0.60,-5.66:6.01	0/0:1:-0.01,-0.31,-1.97:2.96	0/1:3:-3.76,-0.91,-5.29:28.54	0/0:1:-0.00,-0.30,-2.80:3.00	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.90:3.00	1/1:1:-3.77,-0.30,-0.00:3.01	0/1:5:-6.94,-1.51,-8.74:54.28	1/1:1:-3.26,-0.30,-0.00:3.01	./.:-1:0,0,0:-1	1/1:3:-11.80,-0.90,-0.00:9.03
-20	87230	.	G	A	0.34	FDRtranche25.00to35.00+	AB=0.50;AC=3;AF=0.03;AN=98;DB=0;DP=120;Dels=0.00;HRun=4;HaplotypeScore=24.45;MQ=53.77;MQ0=2;OQ=39.98;QD=9.99;SB=-447.00	GT:DP:GL:GQ	0/0:3:-0.00,-0.90,-9.81:9.02	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.60:3.01	0/0:3:-0.00,-0.90,-9.56:9.02	0/0:1:-0.00,-0.30,-3.70:3.01	0/0:1:-0.00,-0.30,-3.57:3.01	0/0:2:-0.00,-0.60,-6.79:6.02	0/0:3:-0.00,-0.90,-10.26:9.03	0/0:3:-0.00,-0.90,-9.51:9.02	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.73:9.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.40:3.01	0/0:1:-0.01,-0.31,-1.87:2.95	0/0:1:-0.00,-0.30,-2.77:3.00	0/0:2:-0.00,-0.60,-7.09:6.02	0/0:2:-0.00,-0.60,-6.36:6.01	0/0:2:-0.00,-0.60,-6.69:6.02	0/0:3:-0.00,-0.90,-9.83:9.02	1/1:2:-5.51,-0.61,-0.01:5.99	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:2:-0.00,-0.60,-6.56:6.01	0/0:2:-0.01,-0.61,-5.56:5.97	0/0:2:-0.00,-0.60,-5.54:6.00	0/0:4:-0.00,-1.21,-12.30:12.02	./.:-1:0,0,0:-1	0/0:5:-0.00,-1.51,-16.43:15.04	0/0:2:-0.00,-0.60,-7.19:6.02	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:3:-0.00,-0.90,-9.83:9.02	0/0:2:-2.85,-2.84,-5.95:2.96	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:1:-0.00,-0.30,-2.57:3.00	0/0:4:-0.00,-1.21,-12.30:12.03	0/0:2:-0.00,-0.60,-6.26:6.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.64:6.01	0/0:3:-0.00,-0.90,-9.43:9.02	0/0:1:-0.00,-0.30,-3.50:3.01	0/1:2:-2.86,-0.60,-3.40:22.52	0/0:2:-0.00,-0.60,-5.74:6.01	0/0:2:-0.00,-0.60,-6.46:6.02	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:2:-0.00,-0.60,-6.16:6.01	0/0:5:-0.01,-1.51,-14.20:14.99	0/0:2:-0.00,-0.60,-6.66:6.02	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.11:9.02
-20	87263	.	G	A	23.48	InDel	AB=0.66;AC=4;AF=0.05;AN=98;DB=0;DP=108;Dels=0.00;HRun=9;HaplotypeScore=28.88;MQ=52.11;MQ0=8;QD=2.61;SB=-436.31	GT:DP:GL:GQ	0/0:3:-0.00,-0.90,-9.96:9.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.40:3.01	./.:-1:0,0,0:-1	0/0:5:-0.00,-1.51,-16.35:15.04	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.76:6.00	0/0:2:-0.00,-0.60,-6.96:6.02	0/0:2:-0.00,-0.60,-6.64:6.02	0/0:4:-0.00,-1.21,-13.33:12.03	0/0:3:-0.00,-0.90,-9.13:9.02	0/0:2:-0.00,-0.60,-6.99:6.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.70:3.01	0/0:1:-0.00,-0.30,-2.87:3.00	0/0:1:-0.00,-0.30,-3.37:3.01	0/0:1:-0.00,-0.30,-2.77:3.00	0/0:5:-0.01,-1.51,-14.17:15.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:2:-0.00,-0.60,-6.36:6.01	0/0:2:-0.00,-0.60,-6.76:6.02	0/0:3:-0.00,-0.90,-8.81:9.01	0/0:2:-0.00,-0.60,-6.34:6.01	0/0:5:-0.00,-1.51,-16.85:15.04	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:1:-0.00,-0.30,-2.97:3.01	0/0:2:-0.00,-0.60,-5.86:6.00	0/0:1:-0.00,-0.30,-3.50:3.01	0/1:5:-2.67,-1.51,-12.53:11.59	0/0:1:-0.00,-0.30,-3.70:3.01	0/0:1:-0.00,-0.30,-3.37:3.01	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:2:-0.00,-0.60,-6.99:6.02	0/0:2:-0.00,-0.60,-6.24:6.01	0/0:1:-0.00,-0.30,-2.97:3.01	0/0:3:-0.00,-0.90,-9.83:9.02	0/0:1:-0.00,-0.30,-2.97:3.01	0/0:1:-0.04,-0.32,-1.37:2.81	0/0:4:-0.00,-1.21,-12.60:12.03	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.90:3.00	./.:-1:0,0,0:-1	0/0:2:-0.02,-0.61,-4.34:5.89	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.76:6.02	1/1:1:-3.87,-0.30,-0.00:3.01	0/1:2:-1.86,-0.62,-3.52:12.32
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-20	99505	.	C	A	0.09	FDRtranche25.00to35.00+	AB=0.60;AC=4;AF=0.05;AN=98;DB=0;DP=94;Dels=0.00;HRun=0;HaplotypeScore=10.68;MQ=58.13;MQ0=0;OQ=14.11;QD=2.02;SB=-400.98	GT:DP:GL:GQ	0/0:3:-0.01,-0.91,-8.66:8.98	0/0:3:-0.00,-0.90,-10.67:9.03	0/0:1:-0.00,-0.30,-3.10:3.01	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.76:3.01	0/1:2:-2.24,-0.60,-3.21:16.35	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:6:-0.01,-1.81,-18.66:18.02	0/0:3:-0.00,-0.90,-9.50:9.02	0/0:4:-0.00,-1.21,-12.22:12.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:2:-0.00,-0.60,-5.50:6.00	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:3:-0.00,-0.90,-9.56:9.02	0/1:4:-2.34,-1.21,-9.36:11.34	0/0:4:-0.05,-1.22,-10.06:11.73	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:1:-0.00,-0.30,-3.36:3.01	0/0:3:-0.00,-0.90,-9.10:9.02	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:6:-0.00,-1.81,-19.46:18.05	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:2:-0.00,-0.60,-6.10:6.01	0/0:1:-0.00,-0.30,-3.06:3.01	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:4:-0.01,-1.21,-11.82:12.00	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:1:-0.00,-0.30,-3.40:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.56:6.02	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-12.86:12.03	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.66:6.02	./.:-1:0,0,0:-1	1/1:1:-2.54,-0.30,-0.00:3.00	0/0:4:-0.00,-1.21,-12.47:12.03	0/0:1:-0.00,-0.30,-3.10:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.82:9.02	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.46:6.02	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:3:-0.00,-0.90,-9.56:9.02
-20	99638	.	A	G	0.37	FDRtranche25.00to35.00+	AB=0.33;AC=1;AF=0.01;AN=98;DB=0;DP=103;Dels=0.00;HRun=1;HaplotypeScore=9.77;MQ=58.54;MQ0=0;OQ=11.22;QD=3.74;SB=-488.90	GT:DP:GL:GQ	0/0:1:-0.00,-0.30,-3.76:3.01	0/1:3:-5.57,-0.91,-3.46:25.55	0/0:2:-0.00,-0.60,-7.63:6.02	0/0:1:-0.00,-0.30,-3.97:3.01	0/0:1:-0.00,-0.30,-3.77:3.01	0/0:1:-0.00,-0.30,-3.47:3.01	0/0:3:-0.00,-0.90,-11.19:9.03	0/0:1:-0.00,-0.30,-2.77:3.00	0/0:1:-0.00,-0.30,-3.97:3.01	0/0:3:-0.00,-0.90,-10.79:9.03	0/0:2:-0.00,-0.60,-6.82:6.02	0/0:2:-0.02,-0.62,-6.03:5.99	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.76:3.01	0/0:1:-0.00,-0.30,-3.87:3.01	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:2:-0.00,-0.60,-7.71:6.02	0/0:6:-0.01,-1.81,-21.49:18.05	0/0:3:-0.00,-0.90,-11.00:9.03	0/0:4:-0.00,-1.21,-14.45:12.04	0/0:2:-0.00,-0.60,-7.81:6.02	./.:-1:0,0,0:-1	0/0:4:-0.00,-1.21,-15.26:12.04	0/0:3:-0.00,-0.90,-11.18:9.03	0/0:2:-0.00,-0.60,-7.42:6.02	0/0:2:-0.00,-0.60,-7.52:6.02	0/0:2:-0.00,-0.60,-7.62:6.02	0/0:4:-0.00,-1.21,-14.56:12.04	0/0:1:-0.00,-0.30,-3.76:3.01	0/0:4:-0.00,-1.21,-13.96:12.03	0/0:3:-0.00,-0.90,-11.49:9.03	0/0:2:-0.00,-0.60,-7.33:6.02	0/0:4:-0.00,-1.21,-14.83:12.04	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.76:3.01	0/0:1:-0.00,-0.30,-3.97:3.01	0/0:1:-0.00,-0.30,-3.57:3.01	0/0:2:-0.00,-0.60,-7.52:6.02	0/0:1:-0.00,-0.30,-3.67:3.01	0/0:1:-0.00,-0.30,-3.77:3.01	0/0:2:-0.00,-0.60,-7.12:6.02	./.:-1:0,0,0:-1	0/0:2:-0.02,-0.62,-5.43:5.98	0/0:1:-0.00,-0.30,-3.47:3.01	0/0:4:-0.00,-1.21,-14.66:12.04	0/0:2:-0.00,-0.60,-7.52:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-7.03:6.02	0/0:2:-0.02,-0.62,-5.82:5.97
-20	99667	.	C	T	43.57	0	AB=0.33;AC=1;AF=0.01;AN=98;DB=0;DP=102;Dels=0.00;HRun=0;HaplotypeScore=15.44;MQ=58.15;MQ0=0;OQ=20.70;QD=6.90;SB=-463.52	GT:DP:GL:GQ	0/0:1:-0.00,-0.30,-3.40:3.01	0/0:2:-0.01,-0.61,-5.79:5.99	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:2:-0.00,-0.60,-6.64:6.02	0/0:2:-0.00,-0.60,-5.94:6.01	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:4:-0.00,-1.20,-14.13:12.04	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:1:-0.00,-0.30,-2.57:3.00	0/0:2:-0.00,-0.60,-7.06:6.02	0/0:2:-0.00,-0.60,-6.76:6.02	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.29:6.01	0/0:4:-0.01,-1.21,-11.20:12.01	0/0:1:-0.00,-0.30,-3.60:3.01	0/0:4:-0.00,-1.21,-13.00:12.03	0/0:3:-0.01,-0.91,-8.03:8.98	0/0:1:-0.00,-0.30,-3.40:3.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:2:-0.00,-0.60,-6.04:6.01	0/0:2:-0.00,-0.60,-6.76:6.02	0/0:3:-0.00,-0.90,-9.43:9.02	0/1:3:-6.56,-0.93,-1.60:6.70	0/0:4:-0.00,-1.21,-13.53:12.03	0/0:2:-0.00,-0.60,-6.26:6.01	0/0:2:-0.00,-0.60,-6.76:6.02	0/0:5:-0.03,-1.52,-13.67:14.88	0/0:2:-0.00,-0.60,-5.54:6.00	0/0:1:-0.00,-0.30,-2.60:3.00	0/0:4:-0.00,-1.21,-12.83:12.02	0/0:1:-0.00,-0.30,-2.47:3.00	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.40:3.01	0/0:1:-0.00,-0.30,-2.97:3.01	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.14:6.01	./.:-1:0,0,0:-1	0/0:5:-0.01,-1.51,-15.33:15.03	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.07:3.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-9.41:9.02	0/0:1:-0.00,-0.30,-2.87:3.00	0/0:1:-0.00,-0.30,-2.70:3.00	0/0:1:-0.00,-0.30,-3.17:3.01	0/0:3:-0.01,-0.91,-9.26:9.01
-20	99701	.	G	T	0.01	FDRtranche25.00to35.00+	AB=0.67;AC=4;AF=0.06;AN=98;DB=0;DP=102;Dels=0.00;HRun=3;HaplotypeScore=13.07;MQ=58.09;MQ0=0;OQ=17.69;QD=1.36;SB=-415.33	GT:DP:GL:GQ	0/0:3:-0.01,-0.91,-9.22:9.00	0/1:3:-2.04,-0.91,-7.06:11.33	0/0:2:-0.00,-0.60,-6.76:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.40:6.00	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.66:3.01	0/0:1:-0.00,-0.30,-3.26:3.01	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.66:6.01	0/0:2:-0.00,-0.60,-6.21:6.01	./.:-1:0,0,0:-1	0/0:1:-0.02,-0.32,-1.76:2.93	1/1:1:-1.59,-0.33,-0.04:2.89	0/1:3:-1.82,-0.93,-4.28:8.89	0/0:1:-0.00,-0.30,-3.56:3.01	0/0:6:-0.01,-1.81,-16.32:17.98	0/0:3:-0.01,-0.91,-7.26:8.94	0/0:2:-0.00,-0.60,-6.40:6.01	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:1:-0.00,-0.30,-3.00:3.01	0/0:1:-0.01,-0.30,-2.36:2.99	0/0:1:-0.00,-0.30,-3.46:3.01	0/0:1:-0.00,-0.30,-3.30:3.01	0/0:4:-0.01,-1.21,-12.37:12.01	0/0:3:-0.04,-0.92,-7.46:8.79	0/0:3:-0.02,-0.92,-8.42:8.95	0/0:3:-0.00,-0.90,-9.16:9.01	0/0:2:-0.00,-0.60,-6.21:6.01	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:3:-0.01,-0.91,-8.52:8.96	0/0:2:-0.00,-0.60,-7.06:6.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.71:6.02	0/0:1:-0.00,-0.30,-3.26:3.01	0/0:3:-0.01,-0.91,-7.96:8.95	0/0:3:-0.01,-0.91,-8.22:8.97	0/0:3:-0.06,-0.93,-6.22:8.75	0/0:4:-0.03,-1.22,-8.66:11.86	0/0:1:-0.00,-0.30,-3.20:3.01	0/0:2:-0.00,-0.60,-6.40:6.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.20:3.01	./.:-1:0,0,0:-1	0/0:3:-0.04,-0.92,-6.96:8.79	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-2.40:2.99
-20	99801	.	G	A	490.97	0	AC=2;AF=0.02;AN=98;DB=0;DP=134;Dels=0.00;HRun=0;HaplotypeScore=11.48;MQ=57.98;MQ0=0;OQ=57.01;QD=19.00;SB=-488.56	GT:DP:GL:GQ	0/0:2:-0.00,-0.60,-6.86:6.02	0/0:3:-0.01,-0.91,-8.53:9.00	./.:-1:0,0,0:-1	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.26:6.01	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.60:3.01	0/0:2:-0.00,-0.60,-6.24:6.01	0/0:1:-0.00,-0.30,-3.27:3.01	0/0:5:-0.00,-1.51,-16.30:15.04	0/0:5:-0.00,-1.51,-17.10:15.04	0/0:3:-0.00,-0.90,-10.69:9.03	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:4:-0.01,-1.21,-11.46:12.01	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:1:-0.00,-0.30,-3.90:3.01	0/0:8:-0.01,-2.41,-24.29:24.04	0/0:5:-0.00,-1.51,-16.95:15.04	0/0:3:-0.00,-0.90,-9.53:9.02	0/0:3:-0.00,-0.90,-10.06:9.02	./.:-1:0,0,0:-1	0/0:1:-0.00,-0.30,-3.07:3.01	0/0:4:-0.00,-1.21,-13.98:12.04	0/0:1:-0.00,-0.30,-3.70:3.01	0/0:4:-0.00,-1.21,-13.03:12.03	0/0:5:-0.00,-1.51,-16.03:15.03	0/0:2:-0.00,-0.60,-6.04:6.01	0/0:3:-0.00,-0.90,-8.61:9.01	0/0:3:-0.00,-0.90,-8.51:9.01	0/0:4:-0.00,-1.21,-12.53:12.02	0/0:4:-0.01,-1.21,-11.93:12.00	0/0:2:-0.00,-0.60,-6.16:6.01	0/0:2:-0.00,-0.60,-6.24:6.01	0/0:3:-0.00,-0.90,-9.96:9.02	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-6.26:6.01	0/0:1:-0.00,-0.30,-3.70:3.01	0/0:2:-0.00,-0.60,-6.66:6.02	0/0:6:-0.00,-1.81,-19.92:18.04	1/1:3:-9.49,-0.93,-0.04:8.97	./.:-1:0,0,0:-1	0/0:2:-0.00,-0.60,-5.84:6.01	./.:-1:0,0,0:-1	0/0:3:-0.00,-0.90,-8.71:9.01	0/0:1:-0.00,-0.30,-3.50:3.01	0/0:2:-0.00,-0.60,-6.36:6.01	0/0:4:-0.00,-1.21,-12.53:12.03	0/0:4:-0.00,-1.21,-12.70:12.03

public/testdata/Beagle/inttestbgl.like

@@ -1,80 +0,0 @@
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-20:77013 C T 0.9406 0.0594 0.0000 0.6657 0.3336 0.0007 0.0001 0.3338 0.6661 0.9419 0.0581 0.0000 0.9990 0.0010 0.0000 0.0001 0.3338 0.6661 0.7992 0.2008 0.0000 0.9394 0.0606 0.0000 0.9693 0.0307 0.0000 0.9844 0.0156 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9406 0.0594 0.0000 0.7992 0.2008 0.0000 0.9844 0.0156 0.0000 0.8882 0.1118 0.0000 0.6658 0.3337 0.0005 0.8859 0.1141 0.0000 0.7992 0.2008 0.0000 0.9693 0.0307 0.0000 0.8029 0.1971 0.0000 0.9844 0.0156 0.0000 0.7992 0.2008 0.0000 0.9840 0.0160 0.0000 0.6653 0.3334 0.0013 0.7992 0.2008 0.0000 0.9406 0.0594 0.0000 0.9844 0.0156 0.0000 0.0011 0.9989 0.0000 0.9406 0.0594 0.0000 0.6660 0.3338 0.0003 0.9844 0.0156 0.0000 0.9840 0.0160 0.0000 0.6616 0.3316 0.0068 0.9918 0.0082 0.0000 0.9394 0.0606 0.0000 0.33 0.33 0.33 0.9406 0.0594 0.0000 0.7955 0.2045 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.6553 0.3361 0.0086 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9687 0.0313 0.0000 
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-20:80481 G C 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.6661 0.3339 0.0000 0.6661 0.3338 0.0001 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.9844 0.0156 0.0000 0.7992 0.2008 0.0000 0.9847 0.0153 0.0000 0.9693 0.0307 0.0000 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.9847 0.0153 0.0000 0.9419 0.0581 0.0000 0.6661 0.3339 0.0000 0.7992 0.2008 0.0000 0.9990 0.0010 0.0000 0.9419 0.0581 0.0000 0.9847 0.0153 0.0000 0.9700 0.0300 0.0000 0.9847 0.0153 0.0000 0.9844 0.0156 0.0000 0.9700 0.0300 0.0000 0.9700 0.0300 0.0000 0.9700 0.0300 0.0000 0.9700 0.0300 0.0000 0.7992 0.2008 0.0000 0.9844 0.0156 0.0000 0.9419 0.0581 0.0000 0.9961 0.0039 0.0000 0.7992 0.2008 0.0000 0.9700 0.0300 0.0000 0.7992 0.2008 0.0000 0.5230 0.4770 0.0000 0.7992 0.2008 0.0000 0.8905 0.1095 0.0000 0.8882 0.1118 0.0000 0.9700 0.0300 0.0000 0.9700 0.0300 0.0000 0.0000 1.0000 0.0000 0.33 0.33 0.33 0.6661 0.3338 0.0000 0.6660 0.3338 0.0001 0.6661 0.3338 0.0000 0.8882 0.1118 0.0000 0.0000 1.0000 0.0000 0.9419 0.0581 0.0000 0.8882 0.1118 0.0000 
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-20:81979 T C 0.33 0.33 0.33 0.0011 0.9985 0.0004 0.33 0.33 0.33 0.6611 0.3313 0.0076 0.6661 0.3338 0.0001 0.6660 0.3338 0.0001 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.6660 0.3338 0.0002 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.6546 0.3357 0.0097 0.6660 0.3338 0.0002 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.33 0.33 0.33 0.0209 0.9784 0.0007 0.0000 0.1971 0.8029 0.33 0.33 0.33 0.6661 0.3338 0.0001 0.6649 0.3332 0.0018 0.6661 0.3338 0.0001 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.33 0.33 0.33 0.6660 0.3338 0.0002 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.0011 0.3335 0.6654 0.33 0.33 0.33 0.33 0.33 0.33 0.9693 0.0307 0.0000 0.0002 0.9998 0.0000 
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-20:82215 G A 0.9693 0.0307 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.0000 0.1971 0.8029 0.8905 0.1095 0.0000 0.7992 0.2008 0.0000 0.8905 0.1095 0.0000 0.9406 0.0594 0.0000 0.0870 0.9106 0.0025 0.7992 0.2008 0.0000 0.6658 0.3337 0.0005 0.33 0.33 0.33 0.6656 0.3336 0.0008 0.0000 0.2008 0.7992 0.6658 0.3337 0.0005 0.33 0.33 0.33 0.33 0.33 0.33 0.6656 0.3336 0.0008 0.33 0.33 0.33 0.6626 0.3321 0.0054 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.0001 0.3338 0.6661 0.33 0.33 0.33 0.6656 0.3336 0.0008 0.0000 0.9840 0.0160 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.6653 0.3334 0.0013 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.6654 0.3335 0.0011 0.6653 0.3334 0.0013 0.6654 0.3335 0.0011 0.0000 0.9800 0.0200 0.6653 0.3334 0.0013 0.33 0.33 0.33 0.33 0.33 0.33 0.0007 0.9894 0.0099 0.9406 0.0594 0.0000 0.6518 0.3343 0.0139 0.8882 0.1118 0.0000 0.6656 0.3336 0.0008 
-20:82217 G A 0.0000 0.0307 0.9693 0.0002 0.3338 0.6660 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.0001 0.3338 0.6661 0.0000 0.1971 0.8029 0.0000 0.1141 0.8859 0.0006 0.3337 0.6658 0.0000 0.1118 0.8882 0.0000 0.0594 0.9406 0.0000 0.2008 0.7992 0.0000 0.2008 0.7992 0.0003 0.3338 0.6659 0.33 0.33 0.33 0.0001 0.3338 0.6661 0.0000 0.1971 0.8029 0.0001 0.3338 0.6661 0.33 0.33 0.33 0.33 0.33 0.33 0.0001 0.3338 0.6660 0.33 0.33 0.33 0.6656 0.3336 0.0008 0.0000 0.2008 0.7992 0.33 0.33 0.33 0.0001 0.3338 0.6661 0.0000 0.2008 0.7992 0.0001 0.3338 0.6661 0.0000 0.1118 0.8882 0.33 0.33 0.33 0.0013 0.9953 0.0034 0.0001 0.3338 0.6661 0.0001 0.3338 0.6661 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.6660 0.3338 0.0002 0.33 0.33 0.33 0.6592 0.3381 0.0027 0.0002 0.3338 0.6660 0.0001 0.3338 0.6661 0.0000 0.2008 0.7992 0.0001 0.3338 0.6661 0.33 0.33 0.33 0.33 0.33 0.33 0.0000 0.2008 0.7992 0.0000 0.9998 0.0002 0.0000 0.2045 0.7955 0.0026 0.9974 0.0000 0.0002 0.3338 0.6660 
-20:82701 T C 0.0007 0.3336 0.6657 0.7992 0.2008 0.0000 0.0000 0.9993 0.0007 0.33 0.33 0.33 0.9844 0.0156 0.0000 0.6660 0.3338 0.0002 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.6661 0.3338 0.0001 0.9419 0.0581 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.6661 0.3338 0.0001 0.7992 0.2008 0.0000 0.9406 0.0594 0.0000 0.6660 0.3338 0.0001 0.0000 0.2008 0.7992 0.7992 0.2008 0.0000 0.0000 0.2008 0.7992 0.9419 0.0581 0.0000 0.0001 0.9999 0.0000 0.0020 0.9980 0.0000 0.0004 0.3337 0.6659 0.7992 0.2008 0.0000 0.0000 0.9983 0.0017 0.0000 1.0000 0.0000 0.8882 0.1118 0.0000 0.6660 0.3338 0.0002 0.8882 0.1118 0.0000 0.9700 0.0300 0.0000 0.0000 1.0000 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.9419 0.0581 0.0000 0.8905 0.1095 0.0000 0.0209 0.9791 0.0000 0.9923 0.0077 0.0000 0.6661 0.3338 0.0001 0.0046 0.3375 0.6580 0.7992 0.2008 0.0000 0.6661 0.3338 0.0001 0.8882 0.1118 0.0000 0.6660 0.3338 0.0002 0.8882 0.1118 0.0000 0.6661 0.3338 0.0001 
-20:87112 G A 0.0000 0.9873 0.0127 0.0000 0.1118 0.8882 0.7992 0.2008 0.0000 0.6658 0.3337 0.0005 0.0000 0.1118 0.8882 0.6654 0.3335 0.0011 0.33 0.33 0.33 0.0000 0.9919 0.0081 0.33 0.33 0.33 0.8029 0.1971 0.0000 0.0000 1.0000 0.0000 0.0005 0.9932 0.0063 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.6659 0.3337 0.0004 0.0001 0.3338 0.6660 0.6658 0.3337 0.0005 0.0000 0.0153 0.9847 0.7992 0.2008 0.0000 0.0000 0.1118 0.8882 0.0000 1.0000 0.0000 0.9693 0.0307 0.0000 0.6654 0.3335 0.0011 0.9923 0.0077 0.0000 0.9406 0.0594 0.0000 0.0000 0.9687 0.0313 0.0000 0.0300 0.9700 0.8882 0.1118 0.0000 0.6657 0.3336 0.0007 0.0000 0.9999 0.0001 0.0000 0.0581 0.9419 0.8882 0.1118 0.0000 0.0000 0.2008 0.7992 0.9693 0.0307 0.0000 0.0021 0.9979 0.0000 0.6654 0.3335 0.0011 0.33 0.33 0.33 0.0011 0.9989 0.0000 0.7992 0.2008 0.0000 0.6613 0.3314 0.0073 0.0014 0.9985 0.0000 0.6654 0.3335 0.0011 0.33 0.33 0.33 0.6656 0.3336 0.0008 0.0001 0.3338 0.6661 0.0000 1.0000 0.0000 0.0004 0.3337 0.6659 0.33 0.33 0.33 0.0000 0.1118 0.8882 
-20:87416 A C 0.0000 0.1118 0.8882 0.0000 0.2008 0.7992 0.6660 0.3338 0.0002 0.6645 0.3331 0.0024 0.0000 0.0300 0.9700 0.0000 0.2008 0.7992 0.7992 0.2008 0.0000 0.0000 0.9884 0.0116 0.0000 0.2008 0.7992 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.6659 0.3337 0.0003 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.0006 0.3337 0.6658 0.33 0.33 0.33 0.33 0.33 0.33 0.0000 0.1095 0.8905 0.9687 0.0313 0.0000 0.0000 0.2008 0.7992 0.33 0.33 0.33 0.0022 0.9960 0.0018 0.0040 0.9950 0.0010 0.0000 0.1118 0.8882 0.33 0.33 0.33 0.0030 0.9579 0.0390 0.0000 0.1118 0.8882 0.8882 0.1118 0.0000 0.0007 0.3336 0.6657 0.8882 0.1118 0.0000 0.0044 0.9956 0.0000 0.0011 0.9980 0.0009 0.33 0.33 0.33 0.0000 0.2008 0.7992 0.0040 0.9960 0.0000 0.33 0.33 0.33 0.6660 0.3338 0.0002 0.0014 0.9968 0.0018 0.0175 0.9825 0.0000 0.0002 0.3338 0.6660 0.0000 0.1118 0.8882 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.0000 0.1118 0.8882 0.7992 0.2008 0.0000 0.0000 0.1165 0.8835 0.8882 0.1118 0.0000 0.0440 0.3340 0.6220 
-20:88155 T C 0.9406 0.0594 0.0000 0.8905 0.1095 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.9406 0.0594 0.0000 0.33 0.33 0.33 0.9406 0.0594 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.9406 0.0594 0.0000 0.9847 0.0153 0.0000 0.9847 0.0153 0.0000 0.7992 0.2008 0.0000 0.9419 0.0581 0.0000 0.9419 0.0581 0.0000 0.6660 0.3338 0.0002 0.8882 0.1118 0.0000 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.9700 0.0300 0.0000 0.9981 0.0019 0.0000 0.9700 0.0300 0.0000 0.8882 0.1118 0.0000 0.9700 0.0300 0.0000 0.9961 0.0039 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9419 0.0581 0.0000 0.7992 0.2008 0.0000 0.9847 0.0153 0.0000 0.9406 0.0594 0.0000 0.9700 0.0300 0.0000 0.9700 0.0300 0.0000 0.8882 0.1118 0.0000 0.9419 0.0581 0.0000 0.6657 0.3336 0.0007 0.9419 0.0581 0.0000 0.9921 0.0079 0.0000 0.9700 0.0300 0.0000 0.7992 0.2008 0.0000 0.0000 0.2008 0.7992 0.9921 0.0079 0.0000 0.6661 0.3338 0.0001 0.7992 0.2008 0.0000 0.9419 0.0581 0.0000 0.9700 0.0300 0.0000 0.9847 0.0153 0.0000 0.9921 0.0079 0.0000 
-20:88827 C A 0.0000 1.0000 0.0000 0.9693 0.0307 0.0000 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.8905 0.1095 0.0000 0.0004 0.3337 0.6659 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.9981 0.0019 0.0000 0.0000 1.0000 0.0000 0.9394 0.0606 0.0000 0.33 0.33 0.33 0.33 0.33 0.33 0.9419 0.0581 0.0000 0.0000 0.9903 0.0097 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.6658 0.3337 0.0005 0.33 0.33 0.33 0.8905 0.1095 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.0000 0.1118 0.8882 0.0029 0.9970 0.0000 0.33 0.33 0.33 0.6659 0.3337 0.0004 0.0000 0.9960 0.0040 0.0002 0.3338 0.6660 0.7992 0.2008 0.0000 0.6659 0.3337 0.0004 0.8882 0.1118 0.0000 0.0016 0.9984 0.0000 0.6659 0.3337 0.0004 0.33 0.33 0.33 0.6659 0.3337 0.0003 0.9419 0.0581 0.0000 0.8882 0.1118 0.0000 0.0000 1.0000 0.0000 0.0000 0.9999 0.0001 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.0000 1.0000 0.0000 0.0011 0.9971 0.0017 0.0029 0.9971 0.0000 0.7992 0.2008 0.0000 0.6658 0.3337 0.0006 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 
-20:88924 A T 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.6661 0.3338 0.0001 0.9844 0.0156 0.0000 0.33 0.33 0.33 0.9693 0.0307 0.0000 0.6661 0.3338 0.0001 0.6660 0.3338 0.0002 0.9847 0.0153 0.0000 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9700 0.0300 0.0000 0.9419 0.0581 0.0000 0.8882 0.1118 0.0000 0.9419 0.0581 0.0000 0.9419 0.0581 0.0000 0.33 0.33 0.33 0.6660 0.3338 0.0002 0.8882 0.1118 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9700 0.0300 0.0000 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.6659 0.3337 0.0004 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.9700 0.0300 0.0000 0.6661 0.3338 0.0001 0.9844 0.0156 0.0000 0.9419 0.0581 0.0000 0.6661 0.3338 0.0001 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.9419 0.0581 0.0000 0.0000 0.1095 0.8905 0.8882 0.1118 0.0000 0.9847 0.0153 0.0000 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.6660 0.3338 0.0002 0.6659 0.3337 0.0004 0.6661 0.3338 0.0001 
-20:89802 T C 0.7879 0.2121 0.0000 0.9406 0.0594 0.0000 0.9847 0.0153 0.0000 0.8882 0.1118 0.0000 0.0000 1.0000 0.0000 0.9700 0.0300 0.0000 0.8882 0.1118 0.0000 0.9700 0.0300 0.0000 0.9847 0.0153 0.0000 0.9847 0.0153 0.0000 0.9406 0.0594 0.0000 0.7992 0.2008 0.0000 0.6630 0.3323 0.0047 0.9923 0.0077 0.0000 0.8882 0.1118 0.0000 0.8882 0.1118 0.0000 0.9961 0.0039 0.0000 0.9700 0.0300 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9419 0.0581 0.0000 0.9923 0.0077 0.0000 0.9923 0.0077 0.0000 0.9847 0.0153 0.0000 0.9923 0.0077 0.0000 0.9961 0.0039 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9693 0.0307 0.0000 0.9844 0.0156 0.0000 0.8882 0.1118 0.0000 0.0418 0.9569 0.0013 0.8882 0.1118 0.0000 0.9981 0.0019 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.9844 0.0156 0.0000 0.9923 0.0077 0.0000 0.9700 0.0300 0.0000 0.9693 0.0307 0.0000 0.7992 0.2008 0.0000 0.9406 0.0594 0.0000 0.7992 0.2008 0.0000 0.8859 0.1141 0.0000 0.9419 0.0581 0.0000 0.9700 0.0300 0.0000 0.9406 0.0594 0.0000 0.9995 0.0005 0.0000 
-20:90008 C A 0.9700 0.0300 0.0000 0.9406 0.0594 0.0000 0.6660 0.3338 0.0003 0.6659 0.3337 0.0004 0.9693 0.0307 0.0000 0.33 0.33 0.33 0.0000 0.0039 0.9961 0.0001 0.9999 0.0000 0.9700 0.0300 0.0000 0.0000 0.0581 0.9419 0.9700 0.0300 0.0000 0.0000 0.9960 0.0040 0.0000 0.2008 0.7992 0.0001 0.3338 0.6661 0.0014 0.9986 0.0000 0.8882 0.1118 0.0000 0.0016 0.9984 0.0000 0.8811 0.1189 0.0000 0.0000 1.0000 0.0000 0.9419 0.0581 0.0000 0.7992 0.2008 0.0000 0.9923 0.0077 0.0000 0.0391 0.9609 0.0000 0.6659 0.3337 0.0003 0.0000 0.9994 0.0006 0.6659 0.3338 0.0003 0.7992 0.2008 0.0000 0.0000 1.0000 0.0000 0.33 0.33 0.33 0.6639 0.3327 0.0033 0.0000 0.9987 0.0013 0.0019 0.9981 0.0000 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.9840 0.0160 0.0000 0.0000 0.0594 0.9406 0.0000 0.0594 0.9406 0.9394 0.0606 0.0000 0.0101 0.9899 0.0000 0.6653 0.3334 0.0013 0.9693 0.0307 0.0000 0.0002 0.3338 0.6660 0.33 0.33 0.33 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.8882 0.1118 0.0000 0.8882 0.1118 0.0000 0.9847 0.0153 0.0000 0.9419 0.0581 0.0000 
-20:90754 A T 0.9960 0.0040 0.0000 0.8882 0.1118 0.0000 0.9419 0.0581 0.0000 0.6660 0.3338 0.0002 0.6661 0.3338 0.0001 0.4036 0.3357 0.2606 0.6660 0.3338 0.0002 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.0000 0.2008 0.7992 0.7955 0.2045 0.0000 0.7992 0.2008 0.0000 0.9700 0.0300 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.9961 0.0039 0.0000 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.6656 0.3336 0.0008 0.9847 0.0153 0.0000 0.8882 0.1118 0.0000 0.9406 0.0594 0.0000 0.6661 0.3338 0.0001 0.9419 0.0581 0.0000 0.8882 0.1118 0.0000 0.8905 0.1095 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9990 0.0010 0.0000 0.9847 0.0153 0.0000 0.8029 0.1971 0.0000 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.9700 0.0300 0.0000 0.9700 0.0300 0.0000 0.9419 0.0581 0.0000 0.6659 0.3338 0.0003 0.33 0.33 0.33 0.9847 0.0153 0.0000 0.7992 0.2008 0.0000 0.9419 0.0581 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.8835 0.1165 0.0000 0.6661 0.3338 0.0001 0.8859 0.1141 0.0000 0.8882 0.1118 0.0000 
-20:90984 A G 0.0000 0.9966 0.0034 0.7992 0.2008 0.0000 0.0000 0.2008 0.7992 0.0067 0.9933 0.0000 0.9406 0.0594 0.0000 0.0027 0.9966 0.0007 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.8859 0.1141 0.0000 0.6660 0.3338 0.0001 0.8882 0.1118 0.0000 0.6661 0.3338 0.0001 0.0000 0.2008 0.7992 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.8882 0.1118 0.0000 0.0025 0.9975 0.0000 0.6659 0.3338 0.0003 0.0086 0.9827 0.0088 0.6660 0.3338 0.0001 0.0041 0.9959 0.0000 0.0000 0.9829 0.0171 0.0053 0.9947 0.0000 0.9419 0.0581 0.0000 0.0000 1.0000 0.0000 0.7992 0.2008 0.0000 0.9921 0.0079 0.0000 0.8882 0.1118 0.0000 0.8882 0.1118 0.0000 0.0021 0.9970 0.0009 0.33 0.33 0.33 0.9693 0.0307 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.0000 1.0000 0.0000 0.0000 1.0000 0.0000 0.6660 0.3338 0.0001 0.33 0.33 0.33 0.0000 1.0000 0.0000 0.6661 0.3338 0.0001 0.0005 0.3337 0.6658 0.9419 0.0581 0.0000 0.8905 0.1095 0.0000 0.6660 0.3338 0.0002 0.6660 0.3338 0.0001 
-20:91088 C T 0.0000 0.0581 0.9419 0.0000 0.2008 0.7992 0.33 0.33 0.33 0.0000 0.2008 0.7992 0.0000 0.1118 0.8882 0.0000 0.2008 0.7992 0.0005 0.3337 0.6658 0.0000 0.2008 0.7992 0.0001 0.3338 0.6661 0.0000 0.1118 0.8882 0.0001 0.3338 0.6661 0.0000 0.0153 0.9847 0.33 0.33 0.33 0.0000 0.2008 0.7992 0.0000 0.0581 0.9419 0.0000 0.2008 0.7992 0.0000 0.2008 0.7992 0.0015 0.3334 0.6652 0.0055 0.9945 0.0000 0.0000 0.1095 0.8905 0.0006 0.3337 0.6658 0.0001 0.3338 0.6660 0.0000 0.2008 0.7992 0.0000 1.0000 0.0000 0.0000 0.2008 0.7992 0.0000 0.2008 0.7992 0.0000 0.0581 0.9419 0.0000 0.1118 0.8882 0.33 0.33 0.33 0.0000 1.0000 0.0000 0.0000 0.2008 0.7992 0.0000 0.0594 0.9406 0.0000 0.1118 0.8882 0.8882 0.1118 0.0000 0.0011 0.9989 0.0000 0.0000 0.0307 0.9693 0.0000 0.0156 0.9844 0.0001 0.3338 0.6661 0.0000 0.0594 0.9406 0.0005 0.3337 0.6658 0.0000 0.2008 0.7992 0.33 0.33 0.33 0.0000 0.0307 0.9693 0.0000 0.2008 0.7992 0.33 0.33 0.33 0.6660 0.3338 0.0002 0.0000 0.2008 0.7992 0.0000 0.1118 0.8882 0.0000 0.1118 0.8882 
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-20:91508 G A 0.0000 0.9892 0.0108 0.0000 0.2008 0.7992 0.33 0.33 0.33 0.0003 0.3338 0.6660 0.0011 0.3335 0.6654 0.33 0.33 0.33 0.0000 0.1118 0.8882 0.0001 0.3338 0.6661 0.0001 0.3338 0.6661 0.0000 0.2008 0.7992 0.0000 0.2008 0.7992 0.0007 0.3336 0.6657 0.0001 0.3338 0.6661 0.33 0.33 0.33 0.0000 0.0581 0.9419 0.0000 0.2008 0.7992 0.0001 0.3338 0.6661 0.0000 0.0307 0.9693 0.6658 0.3337 0.0006 0.33 0.33 0.33 0.7992 0.2008 0.0000 0.0000 0.9873 0.0127 0.0000 0.0581 0.9419 0.0000 1.0000 0.0000 0.0000 0.2008 0.7992 0.0000 0.2008 0.7992 0.0000 0.0300 0.9700 0.0000 0.0156 0.9844 0.0001 0.3338 0.6660 0.0009 0.9991 0.0000 0.0000 0.0581 0.9419 0.0000 0.0300 0.9700 0.0000 0.1118 0.8882 0.7992 0.2008 0.0000 0.9921 0.0079 0.0000 0.0000 0.1118 0.8882 0.0000 0.0156 0.9844 0.0000 1.0000 0.0000 0.0000 0.1118 0.8882 0.0000 0.0300 0.9700 0.0000 0.0300 0.9700 0.33 0.33 0.33 0.0000 0.2008 0.7992 0.0001 0.3338 0.6661 0.33 0.33 0.33 0.0000 0.0581 0.9419 0.0000 0.2008 0.7992 0.0000 1.0000 0.0000 0.0000 0.0153 0.9847 
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-20:93499 T C 0.7992 0.2008 0.0000 0.33 0.33 0.33 0.6652 0.3334 0.0015 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.6661 0.3338 0.0001 0.8905 0.1095 0.0000 0.9847 0.0153 0.0000 0.6660 0.3338 0.0003 0.8882 0.1118 0.0000 0.9406 0.0594 0.0000 0.6661 0.3338 0.0001 0.33 0.33 0.33 0.6660 0.3338 0.0001 0.33 0.33 0.33 0.8882 0.1118 0.0000 0.9700 0.0300 0.0000 0.9406 0.0594 0.0000 0.9419 0.0581 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.6658 0.3337 0.0005 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.6661 0.3338 0.0001 0.9406 0.0594 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.7992 0.2008 0.0000 0.8882 0.1118 0.0000 0.33 0.33 0.33 0.9923 0.0077 0.0000 0.8882 0.1118 0.0000 0.9419 0.0581 0.0000 0.9419 0.0581 0.0000 0.8882 0.1118 0.0000 0.7992 0.2008 0.0000 0.9419 0.0581 0.0000 0.9700 0.0300 0.0000 0.0000 0.0307 0.9693 0.6661 0.3338 0.0001 0.9700 0.0300 0.0000 0.33 0.33 0.33 0.6658 0.3337 0.0005 0.33 0.33 0.33 0.0000 1.0000 0.0000 0.33 0.33 0.33 0.8905 0.1095 0.0000 
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public/testdata/Beagle/inttestbgl.output.vcf

@@ -1,130 +0,0 @@
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-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=OG,Number=1,Type=String,Description="Original Genotype input to Beagle">
-##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
-##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DB,Number=1,Type=Integer,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
-##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=NumGenotypesChanged,Number=1,Type=Integer,Description="r2 Value reported by Beagle on each site">
-##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=R2,Number=1,Type=Float,Description="r2 Value reported by Beagle on each site">
-##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
-##UG_assume_single_sample_reads=null
-##UG_bam_file_used=CEUTSI.chr20.cleaned.bam
-##UG_base_model=EMPIRICAL
-##UG_cap_base_quality_by_mapping_quality=false
-##UG_genotype=false
-##UG_genotype_model=JOINT_ESTIMATE
-##UG_heterozygosity=0.0010
-##UG_max_deletion_fraction=0.05
-##UG_max_mismatches_in_40bp_window=3
-##UG_min_base_quality_score=10
-##UG_min_mapping_quality_score=10
-##UG_noSLOD=false
-##UG_output_all_callable_bases=false
-##UG_platform=null
-##UG_standard_min_confidence_threshold_for_calling=10.0
-##UG_standard_min_confidence_threshold_for_emitting=30.0
-##UG_trigger_min_confidence_threshold_for_calling=30.0
-##UG_trigger_min_confidence_threshold_for_emitting=30.0
-##UG_use_reads_with_bad_mates=false
-##reference=human_g1k_v37.fasta
-##source=BeagleImputation
-##source=UnifiedGenotyper
-##source=VariantOptimizer
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA07056	NA11892	NA11893	NA12347	NA12348	NA12383	NA12413	NA12546	NA12775	NA12777	NA12778	NA20502	NA20505	NA20508	NA20509	NA20510	NA20512	NA20515	NA20516	NA20517	NA20518	NA20519	NA20520	NA20522	NA20524	NA20525	NA20527	NA20528	NA20529	NA20530	NA20531	NA20534	NA20535	NA20538	NA20539	NA20540	NA20541	NA20542	NA20543	NA20544	NA20582	NA20586	NA20588	NA20589	NA20752	NA20753	NA20754	NA20755	NA20756	
-20	60864	.	G	C	20.43	PASS	AB=0.60;AC=1;AF=0.01;AN=98;DB=0;DP=200;Dels=0.00;HRun=0;HaplotypeScore=29.58;MQ=57.91;MQ0=0;NumGenotypesChanged=2;OQ=25.61;QD=5.12;R2=0.815;SB=-529.44	GT:DP:GL:GQ:OG	0|0:5:-0.00,-1.51,-21.02:30.97	0|0:5:-0.00,-1.51,-20.93:30.97	0|0:4:-0.00,-1.21,-16.78:27.99	0|0:3:-0.00,-0.90,-12.59:24.89	0|0:6:-0.00,-1.81,-23.82:33.98	0|0:3:-0.00,-0.90,-12.49:24.89	0|0:2:-0.00,-0.60,-8.38:21.90	0|0:7:-0.05,-2.15,-26.86:36.78	0|0:4:-0.00,-1.21,-15.43:27.99	0|0:10:-0.02,-3.03,-39.69:45.23	0|0:3:-0.00,-0.91,-11.93:24.99	0|0:1:-0.00,-0.30,-4.29:18.93	0|0:.:0,0,0:15.96:./.	0|0:5:-0.00,-1.51,-20.53:30.97	0|0:2:-0.00,-0.60,-8.24:21.90	0|0:1:-0.00,-0.30,-4.19:18.93	0|0:4:-0.00,-1.21,-16.63:27.99	0|0:5:-0.01,-1.51,-17.93:30.86	0|0:1:-0.00,-0.30,-4.29:18.93	0|0:2:-0.00,-0.60,-7.94:21.90	0|0:5:-0.00,-1.51,-22.56:30.97	0|0:9:-0.01,-2.71,-35.06:43.01	0|0:8:-0.00,-2.41,-33.10:40	0|0:2:-0.00,-0.60,-7.94:21.90	0|0:2:-0.00,-0.60,-8.24:21.90	0|0:6:-0.01,-1.81,-22.97:33.87	0|0:3:-0.00,-0.90,-12.63:24.89	0|0:6:-0.03,-1.83,-20.97:33.87	1|0:5:-7.64,-1.51,-11.93:60	0|0:4:-0.00,-1.21,-17.12:27.99	0|0:7:-0.02,-2.13,-26.26:36.99	0|0:3:-0.00,-0.90,-11.79:24.89	0|0:3:-0.00,-0.91,-11.98:24.99	0|0:.:0,0,0:15.96:./.	0|0:8:-0.00,-2.41,-33.55:40	0|0:3:-0.00,-0.90,-12.63:24.89	0|0:1:-0.00,-0.30,-3.75:18.93	0|0:2:-0.00,-0.61,-6.79:22.01	0|0:5:-0.00,-1.51,-19.13:30.97	0|0:1:-0.00,-0.30,-3.55:18.93	0|0:1:-0.00,-0.30,-3.65:18.93	0|0:3:-0.01,-0.91,-11.19:24.89	0|0:5:-0.00,-1.51,-19.13:30.97	0|0:3:-0.00,-0.90,-12.83:24.89	0|0:2:-0.00,-0.60,-7.79:21.90	0|0:4:-0.00,-1.21,-15.58:27.99	0|0:4:-0.01,-1.21,-15.48:27.88	0|0:5:-0.00,-1.51,-20.43:30.97	0|0:5:-0.01,-1.52,-19.02:30.97
-20	61098	rs6078030	C	T	35.52	PASS	AB=0.52;AC=10;AF=0.10;AN=98;DB=1;DP=160;Dels=0.01;HRun=1;HaplotypeScore=43.51;MQ=52.70;MQ0=0;NumGenotypesChanged=5;OQ=365.15;QD=10.14;R2=0.644;SB=-566.38	GT:DP:GL:GQ:OG	0|0:.:0,0,0:16.41:./.	0|0:4:-0.00,-1.20,-13.17:28.51	0|0:2:-0.00,-0.60,-6.76:22.77	0|0:4:-0.01,-1.21,-12.78:26.31	0|0:5:-0.01,-1.51,-15.00:29.67	0|0:1:-0.00,-0.30,-3.40:6.11	0|1:4:-7.95,-1.21,-5.27:60	0|0:4:-0.05,-1.23,-10.60:13.87	0|0:3:-0.00,-0.90,-9.46:25.48	0|1:7:-3.17,-2.11,-19.85:11.80	0|0:7:-0.05,-2.14,-21.69:37.45	0|0:2:-0.00,-0.60,-6.16:20.58	0|0:1:-0.00,-0.30,-2.97:5.99	0|0:4:-0.00,-1.21,-13.96:16.95	0|0:5:-0.00,-1.51,-17.03:30.18	0|0:4:-0.00,-1.21,-13.23:27.99	0|0:4:-0.00,-1.21,-13.43:27.06	0|0:3:-0.00,-0.90,-9.53:25.90	0|0:.:0,0,0:4.13:./.	0|0:1:-0.00,-0.30,-3.50:19.59	1|1:1:-3.16,-0.30,-0.00:1.79	0|0:6:-0.01,-1.81,-18.42:20.08	0|1:10:-16.43,-3.02,-15.44:60	0|0:2:-0.00,-0.60,-6.56:22.65	0|0:2:-0.00,-0.60,-5.44:12.36	0|0:1:-0.00,-0.30,-3.50:6.34	0|0:2:-0.00,-0.60,-5.34:22.85	0|0:2:-0.00,-0.60,-5.74:8.81	0|0:2:-0.00,-0.60,-6.16:9.07	0|0:4:-0.00,-1.21,-14.18:14.73	0|0:3:-0.00,-0.90,-9.96:11.29	0|0:2:-0.00,-0.60,-6.49:22.89	0|0:2:-0.00,-0.60,-6.39:22.28	0|0:.:0,0,0:4.13:./.	0|0:2:-0.00,-0.60,-6.19:13.40	0|0:2:-0.00,-0.60,-5.64:8.34	1|0:3:-2.77,-0.91,-6.17:16.46	0|0:2:-0.00,-0.60,-6.09:21.67	0|1:2:-3.89,-0.61,-1.57:26.88	0|0:4:-0.01,-1.21,-11.76:28.54	1|0:3:-3.07,-0.60,-2.97:22.03	0|0:.:0,0,0:3.76:./.	0|0:3:-0.00,-0.90,-9.66:11.29	0|0:1:-0.00,-0.30,-3.70:16.60	0|0:.:0,0,0:3.84:./.	1|0:4:-7.02,-1.21,-6.79:60	1|0:2:-3.67,-0.60,-3.40:29	0|0:6:-0.00,-1.81,-20.38:19.90	0|0:8:-0.01,-2.41,-26.64:25.87
-20	61421	.	A	C	30.89	PASS	AC=2;AF=0.02;AN=98;DB=0;DP=195;Dels=0.00;HRun=0;HaplotypeScore=13.83;MQ=35.59;MQ0=44;NumGenotypesChanged=7;OQ=21.62;QD=7.21;R2=0.655;SB=-470.00	GT:DP:GL:GQ:OG	0|0:3:-0.00,-0.90,-10.42:32.52	0|0:5:-0.00,-1.51,-18.21:38.86	0|0:1:-0.00,-0.30,-3.79:27.10	0|0:3:-0.00,-0.90,-10.32:30.04	0|0:3:-0.00,-0.90,-9.77:30.36	0|0:5:-0.00,-1.51,-16.15:24.21	0|0:4:-0.00,-1.20,-14.67:33.98	0|0:5:-0.00,-1.51,-16.76:23.25	0|0:.:0,0,0:23.73:./.	0|0:5:-0.00,-1.51,-17.21:22.93	0|0:5:-0.00,-1.51,-19.02:38.86	0|0:5:-0.01,-1.51,-14.79:36.38	0|0:1:-0.00,-0.30,-3.14:11.83	0|0:3:-0.00,-0.90,-10.83:20.11	0|1:1:-3.06,-0.30,-0.00:18.23:1/1	0|0:1:-0.00,-0.30,-3.69:25.95	0|0:1:-0.00,-0.30,-3.69:24.78	0|0:3:-0.00,-0.90,-9.53:33.28	0|0:2:-0.00,-0.60,-6.28:16.14	0|0:2:-0.00,-0.60,-6.59:29.83	0|0:2:-0.00,-0.60,-6.58:16.67	0|0:2:-0.00,-0.60,-6.58:14.17	0|0:3:-0.01,-0.91,-8.92:17.19	0|0:2:-0.00,-0.60,-6.43:29.91	0|0:3:-0.00,-0.90,-9.93:21.63	0|0:1:-0.00,-0.30,-3.44:12.38	0|0:1:-0.00,-0.30,-3.59:27.24	0|0:1:-0.00,-0.30,-3.44:11.88	0|0:.:0,0,0:9.15:./.	0|0:.:0,0,0:8.74:./.	0|0:3:-0.00,-0.90,-10.17:17.36	0|0:3:-0.00,-0.90,-9.72:33.28	0|0:2:-0.00,-0.60,-6.33:29.43	0|0:2:-0.00,-0.60,-6.18:16.14	0|0:3:-0.00,-0.90,-9.22:22.80	0|0:1:-0.00,-0.30,-2.64:11.32	0|0:.:0,0,0:16.07:./.	0|0:3:-0.00,-0.90,-10.02:31.61	0|0:1:-0.00,-0.30,-3.34:24.80	0|0:2:-0.00,-0.60,-7.13:29.79	0|1:1:-2.96,-0.30,-0.00:17.54:1/1	0|0:1:-0.00,-0.30,-3.24:12.49	0|0:3:-0.00,-0.90,-9.72:17.36	0|0:.:0,0,0:20.13:./.	0|0:1:-0.01,-0.30,-2.14:12.53	0|0:4:-0.00,-1.20,-13.31:34.56	0|0:5:-0.00,-1.51,-17.05:36.99	0|0:2:-0.00,-0.60,-6.63:13.91	0|0:5:-0.00,-1.51,-16.95:23.08
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public/testdata/Beagle/inttestbgl.phased

@@ -1,80 +0,0 @@
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-M 20:60864 G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G C G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G
-M 20:61098 C C C C C C C C C C C C C T C C C C C T C C C C C C C C C C C C C C C C C C C C T T C C C T C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C T C C T C C C C C C C C C T C T C C C C C
-M 20:61421 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A
-M 20:61795 G G G G G G G G G G G T G T G T G G T T G G G G G T T G G T G G G G G G T G G G T T T G T T G G G G G T G G G T T G T G G T G G G G G T G G G T T G G G G T G G T T T G T G G G G T T G T G T G T G
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-M 20:91088 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T C T C T T T C T T T T T T T T T T T C T T T T T T T C T C T T T T T T C T T T T T T T T T T T T T T C T T T C T T T
-M 20:91346 G A G G A A A G G G G A G G G G G G G G G A G G G G G G G G G A G G G G G G G A G G G A G G G A G A A G G G G A A G G G G G G G A G G A G G G G G G G G A G A G G G G G G A A G G A G G G G G G G G
-M 20:91508 G A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G A A A G A G A A A G A A A A A A A A A A A G A A A A A A A G A G G A A A A A G A A A A A A A A A A A A A A A A A A G A A A
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-M 20:92366 G G G G A A A A G G A A A A G A A A A A A G A A G A G G A A G A A G G G A A G G A G A A A G A A A A A A G G A A A A G A A G A G G A A A G A A A A A A A A A A A A A A A A A A A G A G G A G A G G G
-M 20:92527 G G G G G A G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G A G G G A G G A G G G A G G G G G G G G G G A G G G G G G G G G G G G G G G A G G G G G G G G G G G G G G G A G G G A G G G
-M 20:92865 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T T T T T C T T T T
-M 20:92891 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G G A A A A A A A A A A A A A A A A
-M 20:93440 A G A A A A A A A A G G A G A A A A A A A G A A A A A A A A G A A A A A A A A A A A G A A A A A A G G G A A G G G G A A A A A A G A A G A A A A A A A A A G G A A A A A G A G A G A A A A A A A A A
-M 20:93499 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C C T T T T T T T T T T T C T T T T
-M 20:93863 G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G A G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G A
-M 20:93931 G A G G G G G A G G G G G G G G G G G G G A G G G G G G G G A G G G G G G G G G G G A G G G G G G G G A G G G A G G G G G G G G A G G G G G G G G G G G G A A G G G G G A G A G A G G G G G G G G G
-M 20:94091 T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C C T T T T T T T T T T T C T T T T
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-M 20:96931 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G A A A A A A A A A A A G A A A A G A A A G A A A G A A A A A A A A G A A A A A A A A A A A A G G A G A A A G A G A G A A A A G A A A A
-M 20:97122 C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C C C C C C C C T C C C C T C C C T C C C T C C C C C C C C T C C C C C C C C C C C C T T C C C C C T C T C T C C C C C C C C C
-M 20:97227 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A C A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A
-M 20:97394 A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A G A A A A A A A A A A A G A A A A A A A A G A A A G A A A A A A A A A A A A A A A A A A A A A A G A G A A A G A G A G A A A A G A A A A
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-M 20:98930 G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G A G G G G G G G G G G G A G G G G A G G G A G G G A G G G G G G G G A G G G G G G G G G G G G A A G G G G G A G A G A G G G G G G G G G
-M 20:99667 C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C T C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C
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-20:75254	0.834
-20:76962	0.751
-20:77013	0.790
-20:77816	0.823
-20:79234	0.385
-20:80071	0.596
-20:80481	0.758
-20:80655	0.731
-20:80728	0.624
-20:81666	0.547
-20:81979	0.217
-20:82079	0.378
-20:82215	0.329
-20:82217	0.376
-20:82701	0.672
-20:87112	0.653
-20:87416	0.629
-20:88155	0.835
-20:88827	0.663
-20:88924	0.652
-20:89802	0.664
-20:90008	0.770
-20:90754	0.797
-20:90984	0.785
-20:91088	0.646
-20:91346	0.800
-20:91508	0.733
-20:91707	0.609
-20:91716	0.668
-20:92366	0.649
-20:92527	0.658
-20:92865	0.794
-20:92891	0.900
-20:93440	0.499
-20:93499	0.968
-20:93863	0.529
-20:93931	0.620
-20:94091	0.967
-20:94528	0.976
-20:94592	0.793
-20:94952	0.886
-20:95052	0.866
-20:95093	0.686
-20:96166	0.908
-20:96298	0.867
-20:96931	0.956
-20:97122	0.921
-20:97227	0.780
-20:97394	0.764
-20:97395	0.901
-20:98930	0.945
-20:99667	0.606
-20:99801	0.656

public/testdata/GIH.samples.list

@@ -1,70 +0,0 @@
-NA20845
-NA20846
-NA20847
-NA20849
-NA20850
-NA20851
-NA20852
-NA20853
-NA20854
-NA20856
-NA20858
-NA20859
-NA20861
-NA20862
-NA20863
-NA20864
-NA20866
-NA20867
-NA20868
-NA20869
-NA20870
-NA20871
-NA20872
-NA20873
-NA20874
-NA20875
-NA20876
-NA20877
-NA20881
-NA20885
-NA20886
-NA20887
-NA20888
-NA20889
-NA20890
-NA20891
-NA20892
-NA20894
-NA20895
-NA20896
-NA20897
-NA20898
-NA20899
-NA20901
-NA20902
-NA20903
-NA20904
-NA20906
-NA20908
-NA20910
-NA20911
-NA21086
-NA21088
-NA21089
-NA21090
-NA21091
-NA21092
-NA21094
-NA21097
-NA21098
-NA21099
-NA21100
-NA21101
-NA21102
-NA21103
-NA21137
-NA21141
-NA21142
-NA21143
-NA21144

public/testdata/MendelianViolationEval.ped

@@ -1,6 +0,0 @@
-TRIO	TRIO_MOTHER	0	0	0	-9
-TRIO	TRIO_FATHER	0	0	1	-9
-TRIO	TRIO_CHILD	TRIO_MOTHER	TRIO_FATHER	0	-9
-PAIR	PAIR_PARENT	0	0	0	-9
-PAIR	PAIR_CHILD	PAIR_PARENT	0	1	-9
-UNRELATED	UNRELATED_INDIVIDUAL_CONTROL	0	0	0	-9

public/testdata/MendelianViolationEval.vcf

@@ -1,22 +0,0 @@
-##fileformat=VCFv4.0
-##MendelianViolationEvaluator="This file contains genotypes with mendelian violations in the input data. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_PARENT	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
-1	10109	.	A	T	99	PASS	.	GT:GQ:PL	0/0:50:0,50,200	0/0:40:0,40,200	0/1:30:30,0,200	0/0:50:0,50,200	0/1:30:30,0,200	0/0:50:0,50,200	
-1	10147	.	C	A	99	PASS	.	GT:GQ:PL	0/0:30:0,30,200	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200	
-1	10150	.	C	T	99	PASS	.	GT:GQ:PL	0/0:40:0,40,200	0/1:30:30,0,200	1/1:50:200,50,0	0/0:40:0,40,200	1/1:50:200,50,0	0/0:40:0,40,200
-1	10177	.	A	C	99	PASS	.	GT:GQ:PL	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	0/0:50:0,50,200	0/0:30:0,30,200	0/0:50:0,50,200
-1	10180	.	T	C	99	PASS	.	GT:GQ:PL	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200
-1	10234	.	C	T	99	PASS	.	GT:GQ:PL	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/1:40:40,0,200	1/1:50:200,50,0	0/1:40:40,0,200
-1	10235	.	T	A	99	PASS	.	GT:GQ:PL	0/1:50:50,0,200	1/1:40:200,40,0	0/0:30:0,30,200	0/1:50:50,0,200	0/0:30:0,30,200	0/1:50:50,0,200
-1	10236	.	A	G	99	PASS	.	GT:GQ:PL	1/1:30:200,30,0	0/0:50:0,50,200	0/0:40:0,40,200	1/1:30:200,30,0	0/0:50:0,50,200	1/1:30:200,30,0
-1	10250	.	A	C	99	PASS	.	GT:GQ:PL	1/1:40:200,40,0	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	1/1:50:200,50,0	1/1:40:200,40,0
-1	10257	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/0:30:0,30,200	1/1:50:200,50,0
-1	10285	.	T	C	99	PASS	.	GT:GQ:PL	1/1:30:200,30,0	1/1:50:200,50,0	0/1:40:40,0,200	1/1:30:200,30,0	0/1:40:40,0,200	1/1:30:200,30,0
-1	10297	.	C	T	99	PASS	.	GT:GQ:PL	1/1:40:200,40,0	1/1:30:200,30,0	0/0:50:0,50,200	1/1:40:200,40,0	0/0:50:0,50,200	1/1:40:200,40,0
-1	10304	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:0:0,0,0	1/1:50:200,50,0	0/1:0:0,0,0	1/1:50:200,50,0
-1	10304	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	1/1:50:200,50,0
-1	10310	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0
-1	10315	.	C	T	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0

public/testdata/MultiSample.vcf

@@ -1,103 +0,0 @@
-##source=UnifiedGenotyper
-##format=VCRv3.2
-##reference=human_b36_both.fasta
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA11894	NA11992	NA06994	NA07037	NA12760	NA12761	NA12414	NA12762	NA12716	NA12717	NA10851	NA11919	NA11918	NA07347	NA12873	NA12874	NA06986	NA06985	NA07346	NA12763	NA11994	NA11993	NA11995	NA11840	NA12234	NA07000	NA12003	NA07357	NA11920	NA12287	NA12144	NA07051	NA12828	NA12776	NA12044	NA11831	NA11830	NA12045	NA12872	NA12489	NA11881	NA12043	NA11832	NA12751	NA12750	NA11931	NA12155	NA12154	NA12249	NA12156	NA12815	NA11829	NA12749	NA12812	NA12813	NA12814	NA12004	NA12005	NA10847	NA12006	
-1	10000005	.	A	T	0.00	.	AF=0.01;NS=60;SB=0.22	GT:RD:GQ	./.	0/0:5:3.00	0/0:2:2.11	0/0:2:2.14	./.	0/0:1:1.84	0/0:1:1.83	0/0:1:1.84	0/0:5:3.04	0/0:1:1.83	0/0:7:3.40	./.	./.	./.	0/0:1:1.84	0/0:4:2.74	0/0:6:3.34	0/0:2:1.91	0/0:3:2.43	0/0:1:1.84	0/0:1:1.84	0/0:1:1.83	./.	0/0:3:2.44	0/0:1:1.84	0/0:2:2.10	0/0:1:1.83	0/0:5:3.03	0/0:9:3.71	0/1:2:1.54	0/0:2:1.90	0/0:2:2.14	0/0:1:1.84	0/0:1:1.83	./.	0/0:6:3.27	0/0:5:2.51	0/0:4:2.49	0/0:3:2.44	0/0:2:2.06	0/0:4:2.74	0/0:1:1.84	0/0:3:2.06	0/0:1:1.83	0/0:1:1.84	./.	0/0:9:4.23	0/0:3:1.92	0/0:2:2.14	0/0:1:1.84	0/0:2:2.14	0/0:4:2.44	0/0:1:1.84	0/0:2:2.14	0/0:1:1.84	0/0:1:1.84	0/0:1:1.83	./.	0/0:1:1.84	0/0:1:1.84
-1	10000007	.	T	A	8.15	.	AF=0.01;NS=60;SB=0.21	GT:RD:GQ	./.	0/0:4:2.42	0/0:2:1.71	0/0:2:2.12	./.	0/0:1:1.82	0/0:1:1.82	0/0:2:1.73	0/0:4:2.72	0/0:1:1.82	0/0:7:3.29	./.	./.	0/0:1:1.82	0/0:1:1.82	0/0:4:2.72	0/0:4:2.72	0/0:2:2.07	0/0:2:2.12	0/0:1:1.82	./.	./.	./.	0/0:3:2.42	0/0:1:1.82	0/0:3:2.12	0/0:1:1.82	0/0:6:2.73	0/0:8:3.27	1/0:2:1.52	0/0:2:1.67	0/0:2:2.12	0/0:1:1.82	0/0:1:1.82	./.	0/0:6:3.33	0/0:4:2.72	0/0:4:2.72	0/0:3:2.42	0/0:3:2.12	0/0:4:2.72	0/0:1:1.82	0/0:2:2.12	0/0:1:1.82	0/0:1:1.82	0/0:1:1.82	0/0:8:3.93	0/0:3:2.01	0/0:2:2.12	./.	0/0:2:2.12	0/0:4:2.42	0/0:1:1.82	0/0:2:2.12	0/0:2:1.58	0/0:1:1.82	0/0:1:1.82	./.	0/0:1:1.82	0/0:1:1.82
-1	10000065	.	C	G	0.00	.	AF=0.01;NS=60;SB=2.50	GT:RD:GQ	0/0:2:2.33	0/0:8:4.13	0/0:3:2.63	0/0:5:3.23	0/0:4:2.92	0/1:3:0.82	0/0:5:3.23	0/0:3:2.63	0/0:6:3.53	0/0:2:2.33	0/0:8:4.13	0/0:1:1.91	0/0:2:2.33	0/0:2:2.33	0/0:1:2.03	0/0:6:3.53	0/0:10:4.73	0/0:2:2.33	0/0:4:2.93	0/0:2:2.33	./.	./.	0/0:6:3.53	0/0:4:2.89	0/0:1:2.03	0/0:3:2.63	0/0:5:3.23	0/0:5:3.23	0/0:8:4.13	0/0:5:3.23	0/0:13:5.33	0/0:7:3.82	0/0:1:2.03	0/0:2:2.33	0/0:1:2.03	0/0:3:2.63	0/0:5:3.23	0/0:1:2.03	0/0:3:2.63	0/0:2:2.09	0/0:3:2.63	0/0:2:2.33	0/0:3:2.63	0/0:4:2.93	0/0:2:2.33	0/0:4:2.93	./.	0/0:2:2.32	0/0:3:2.63	0/0:4:2.93	0/0:4:2.93	0/0:3:2.62	0/0:2:2.32	0/0:4:2.93	0/0:2:2.33	0/0:1:2.03	./.	0/0:2:2.33	0/0:1:2.03	0/0:6:3.53
-1	10000074	.	T	C	2.32	.	AF=0.01;NS=60;SB=-0.24	GT:RD:GQ	0/0:2:2.42	0/0:8:4.22	0/0:2:2.19	0/0:6:3.62	0/0:3:2.72	0/0:4:2.90	0/0:5:3.32	0/0:3:2.72	0/0:6:3.37	0/0:4:3.01	0/0:9:4.22	0/0:1:2.12	1/0:2:0.38	0/0:2:2.42	0/0:1:2.12	0/0:6:3.62	0/0:12:3.77	0/0:1:2.12	0/0:4:3.02	0/0:2:2.39	0/0:1:2.12	0/0:2:2.19	0/0:5:3.29	0/0:4:3.00	0/0:1:2.12	0/0:4:2.98	0/0:4:3.02	0/0:7:3.92	0/0:10:4.65	0/0:5:2.43	0/0:7:3.92	0/0:7:3.92	./.	0/0:1:2.12	./.	0/0:3:2.71	0/0:5:3.32	0/0:1:2.12	0/0:3:2.72	0/0:2:2.42	0/0:3:2.72	0/0:3:2.72	0/0:1:2.09	0/0:4:3.00	0/0:2:2.42	0/0:4:3.02	./.	0/0:1:2.12	0/0:1:2.12	0/0:5:3.09	0/0:3:2.72	0/0:1:2.12	0/0:4:2.72	0/0:4:3.02	0/0:1:2.06	0/0:1:2.12	0/0:1:2.12	0/0:2:2.42	0/0:1:2.12	0/0:5:3.32
-1	10000078	.	G	C	0.00	.	AF=0.01;NS=60;SB=2.32	GT:RD:GQ	0/0:2:2.28	0/0:8:3.79	0/0:1:1.98	0/0:6:3.49	0/0:3:2.58	0/0:4:2.87	0/0:5:3.18	0/0:3:2.28	0/0:6:3.48	0/0:4:2.87	0/0:7:3.39	0/0:1:1.98	0/0:2:2.28	0/0:2:2.28	0/0:1:1.98	0/0:6:3.49	0/0:11:4.99	0/0:1:1.98	0/0:4:2.88	0/0:2:2.28	0/0:1:1.98	1/0:2:1.11	0/0:5:3.18	0/0:4:2.85	0/0:1:1.98	0/0:4:2.88	0/0:4:2.88	0/0:7:3.79	0/0:9:3.78	0/0:5:3.18	0/0:5:2.88	0/0:5:3.18	./.	0/0:1:1.98	./.	0/0:3:2.57	0/0:5:3.18	0/0:1:1.98	0/0:3:2.58	0/0:2:2.28	0/0:3:2.58	0/0:3:2.58	0/0:1:1.98	0/0:4:2.88	0/0:2:2.27	0/0:4:2.88	./.	0/0:1:1.68	0/0:2:2.28	0/0:4:2.39	0/0:3:2.58	0/0:1:1.98	0/0:2:2.27	0/0:4:2.88	0/0:1:1.98	0/0:1:1.98	0/0:1:1.98	0/0:2:2.28	0/0:1:1.98	0/0:7:3.66
-1	10000080	.	C	T	20.08	.	AF=0.02;NS=60;SB=-1.74	GT:RD:GQ	0/0:2:1.92	0/0:8:3.58	0/0:1:1.62	0/0:6:3.12	0/0:2:1.90	0/0:4:2.52	0/0:4:2.52	0/0:2:1.92	0/0:5:2.76	0/0:4:2.48	0/0:8:3.69	0/0:1:1.62	0/0:2:1.92	0/0:2:1.31	0/0:1:1.62	0/0:6:3.12	0/0:11:4.62	0/0:1:1.62	0/0:4:2.51	0/0:2:1.91	0/0:1:1.62	0/0:2:1.92	0/0:5:2.39	0/0:4:2.46	0/0:1:1.62	0/0:4:2.52	0/0:4:1.99	0/0:6:3.12	0/1:7:4.36	0/0:5:2.81	0/0:4:2.22	0/0:5:2.33	./.	0/0:1:1.62	./.	0/0:3:2.16	0/0:5:2.81	0/0:1:1.62	0/0:3:2.22	0/0:2:1.92	0/0:3:2.21	0/0:3:2.22	0/0:1:1.54	0/0:4:2.49	./.	0/0:3:2.22	./.	./.	0/1:2:2.04	0/0:4:2.52	0/0:3:2.22	0/0:1:1.62	0/0:2:1.92	0/0:4:2.52	0/0:1:1.62	0/0:1:1.62	0/0:1:1.62	0/0:2:1.92	./.	0/0:7:3.41
-1	10000092	.	G	A	0.00	.	AF=0.01;NS=60;SB=2.81	GT:RD:GQ	0/0:2:2.21	0/0:5:2.98	./.	0/0:8:4.00	./.	0/0:4:2.81	0/0:1:1.91	0/0:2:2.10	0/0:3:2.51	0/0:5:2.50	0/0:3:2.49	0/0:1:1.90	0/0:2:2.20	0/0:1:1.87	0/0:1:1.91	0/0:4:2.81	0/0:7:0.51	0/0:1:1.61	0/0:1:1.91	0/0:1:1.90	0/0:1:1.91	0/0:2:2.21	0/0:1:1.91	0/0:2:2.21	0/0:1:1.91	0/0:3:1.61	0/0:2:2.21	0/0:5:2.80	0/0:4:2.38	0/0:5:3.11	0/0:3:2.51	0/0:4:2.81	./.	0/0:1:1.91	0/0:2:2.21	0/0:2:2.20	0/0:3:2.51	0/0:1:1.91	0/0:3:2.51	0/0:2:2.21	0/0:4:2.81	0/0:3:2.51	./.	0/0:6:3.41	./.	0/0:3:2.51	./.	0/0:1:1.91	0/0:4:2.80	0/0:3:2.51	0/0:3:2.50	0/0:3:2.51	0/0:2:2.21	0/0:4:2.81	0/0:2:2.21	0/0:2:2.21	0/0:1:1.91	0/0:1:1.91	./.	1/0:5:0.44
-1	10000102	.	A	G	0.00	.	AF=0.01;NS=60;SB=2.66	GT:RD:GQ	0/0:1:1.98	0/0:2:1.97	./.	0/0:7:3.78	./.	0/0:5:3.18	0/0:1:1.97	./.	0/0:1:1.98	0/0:4:2.65	0/0:4:2.88	0/0:2:2.28	0/0:2:2.28	0/0:1:1.98	0/0:1:1.98	0/0:4:2.88	0/0:4:2.74	0/0:1:1.98	./.	./.	0/0:1:1.98	0/0:2:2.28	0/0:1:1.98	0/0:2:2.28	0/0:1:1.98	0/0:2:2.28	0/0:1:1.98	0/0:6:3.48	0/0:3:1.98	0/0:4:2.88	0/0:5:3.18	0/0:3:2.58	./.	./.	0/0:3:2.58	0/0:1:1.97	0/0:2:2.28	0/0:2:2.28	0/0:3:2.58	0/0:1:1.98	0/0:6:3.18	0/0:4:2.88	0/0:1:1.98	0/0:5:3.18	./.	0/0:2:2.28	0/0:2:2.28	0/0:1:1.98	0/0:4:2.88	0/0:2:2.27	0/0:3:2.58	0/0:2:2.28	0/0:1:1.98	0/0:5:3.18	0/0:2:2.28	0/0:2:2.28	0/0:2:2.28	0/1:1:0.62	0/0:1:1.98	0/0:4:2.88
-1	10000110	.	G	C	0.00	.	AF=0.02;NS=60;SB=2.88	GT:RD:GQ	0/0:1:1.81	0/0:3:2.41	0/0:1:1.81	0/0:8:3.92	./.	0/0:7:3.62	0/0:1:1.81	./.	0/0:1:1.81	0/0:1:1.81	0/0:8:3.86	0/0:2:2.11	0/0:1:1.81	0/0:2:2.11	0/0:1:1.81	0/0:4:2.71	0/0:6:3.31	0/0:1:1.81	0/0:1:1.70	0/0:2:2.10	0/0:1:1.81	0/0:1:1.81	0/0:1:1.81	0/0:2:2.11	0/0:1:1.81	0/0:4:2.11	0/0:1:1.81	1/0:5:0.30	0/0:4:2.41	0/0:4:2.71	0/0:8:3.62	0/0:2:2.11	./.	./.	0/0:2:2.11	0/0:1:1.81	1/0:3:0.12	0/0:2:2.11	0/0:3:2.41	./.	0/0:8:3.92	0/0:4:2.71	0/0:1:1.81	0/0:7:3.62	0/0:1:1.81	0/0:1:1.81	0/0:2:2.11	0/0:2:1.81	0/0:3:2.41	./.	0/0:3:2.41	0/0:1:1.79	0/0:1:1.81	0/0:5:3.01	0/0:1:1.81	0/0:2:2.11	0/0:1:1.81	0/0:1:1.81	0/0:3:2.41	0/0:4:2.71
-1	10000112	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.37	GT:RD:GQ	0/0:1:1.94	1/0:2:1.09	0/0:2:2.24	0/0:8:4.04	./.	0/0:7:3.74	0/0:1:1.94	./.	0/0:3:2.54	0/0:1:1.94	0/0:8:4.01	0/0:2:2.24	0/0:2:2.24	0/0:2:2.24	0/0:2:2.24	0/0:4:2.84	0/0:6:3.43	0/0:1:1.94	0/0:1:1.82	0/0:2:2.23	0/0:1:1.94	0/0:1:1.94	0/0:1:1.94	0/0:2:2.24	0/0:1:1.94	0/0:4:2.84	0/0:1:1.94	0/0:5:2.83	0/0:5:2.84	0/0:5:3.14	0/0:7:3.74	0/0:1:1.94	./.	./.	0/0:2:2.24	0/0:2:2.24	0/0:4:2.84	0/0:2:2.24	0/0:3:2.54	0/0:1:1.64	0/0:8:4.04	0/0:4:2.84	0/0:1:1.94	0/0:7:3.23	0/0:2:2.24	0/0:1:1.94	0/0:3:2.53	0/0:2:2.24	0/0:4:2.84	./.	0/0:3:2.54	0/0:1:1.82	0/0:2:2.23	0/0:5:3.14	0/0:1:1.64	0/0:2:2.24	0/0:2:2.24	0/0:1:1.93	0/0:3:2.54	0/0:4:2.84
-1	10000118	.	G	A	1.11	.	AF=0.01;NS=60;SB=-0.12	GT:RD:GQ	0/0:2:2.50	0/0:5:3.05	0/0:2:2.50	0/0:7:3.99	./.	0/0:6:3.71	0/0:3:2.80	0/0:1:1.90	0/0:5:3.41	0/0:2:2.50	0/0:8:4.22	0/0:3:2.80	0/0:2:2.50	0/0:3:2.80	0/0:2:2.49	0/0:4:3.10	0/0:7:2.88	./.	0/0:2:1.61	0/0:4:3.10	0/0:1:2.20	0/0:2:2.50	./.	0/0:1:2.20	0/0:1:2.20	0/0:3:2.50	0/0:1:2.20	0/0:4:3.11	0/0:9:4.61	0/0:5:3.39	0/0:5:3.41	0/0:2:2.50	0/0:1:2.20	0/0:1:2.20	0/0:1:2.20	0/0:3:2.80	0/0:5:3.41	0/0:2:2.41	0/0:3:2.81	0/0:1:2.20	0/0:8:4.31	0/0:6:3.71	0/0:1:2.20	0/0:8:4.30	1/0:2:0.06	0/0:1:2.20	0/0:3:2.78	0/0:2:2.50	0/0:4:3.10	0/0:1:1.90	0/0:3:2.80	0/0:1:2.18	0/0:3:2.80	0/0:5:3.41	./.	0/0:2:2.50	0/0:2:2.50	./.	0/0:3:2.80	0/0:3:2.81
-1	10000119	.	T	A	1.37	.	AF=0.01;NS=60;SB=-0.14	GT:RD:GQ	0/0:2:2.48	1/0:5:0.14	0/0:3:2.47	0/0:6:3.66	./.	0/0:6:3.67	0/0:4:2.90	0/0:1:2.18	0/0:5:3.37	0/0:2:2.26	0/0:8:3.88	0/0:3:2.77	0/0:2:2.36	0/0:3:2.78	0/0:2:2.48	0/0:4:3.08	0/0:9:3.93	./.	0/0:2:2.45	0/0:4:3.07	./.	0/0:2:2.48	./.	0/0:1:2.18	0/0:1:2.18	0/0:3:2.48	0/0:2:2.48	0/0:5:2.10	0/0:9:4.57	0/0:5:3.38	0/0:7:3.38	0/0:2:2.48	0/0:1:2.18	0/0:1:2.18	./.	0/0:3:2.77	0/0:5:3.38	0/0:3:2.76	0/0:3:2.78	0/0:1:2.18	0/0:8:4.28	0/0:6:3.50	0/0:1:2.18	0/0:8:2.57	0/0:3:2.76	0/0:1:2.18	0/0:3:2.78	0/0:2:2.47	0/0:5:3.38	0/0:1:2.18	0/0:3:2.78	0/0:1:2.18	0/0:3:2.78	0/0:5:3.38	./.	0/0:2:2.48	0/0:2:2.48	./.	0/0:3:2.78	0/0:3:2.78
-1	10000171	.	C	G	1.67	.	AF=0.01;NS=60;SB=-0.17	GT:RD:GQ	0/0:3:2.59	0/0:4:3.11	0/0:3:2.81	0/0:2:2.51	./.	0/0:4:3.11	0/0:10:4.32	0/0:3:2.81	0/0:4:3.11	0/0:5:3.42	0/0:11:5.22	0/0:5:3.41	0/0:1:2.21	0/0:3:2.81	0/0:5:3.42	0/0:2:2.51	0/0:10:4.92	0/0:2:2.51	0/0:1:2.21	0/0:3:2.81	0/0:2:2.51	0/0:5:3.11	0/0:2:2.51	0/0:2:2.51	0/0:1:2.21	0/0:10:4.92	0/0:4:3.11	0/0:2:2.51	0/0:10:4.18	0/0:4:3.12	0/0:7:4.02	0/0:8:4.32	0/0:3:2.81	./.	0/0:5:3.42	0/0:4:2.81	0/0:4:3.06	0/0:3:2.81	0/0:3:2.81	0/0:6:3.70	0/0:6:3.72	0/0:3:2.81	0/0:8:4.32	0/0:5:3.42	0/0:4:3.11	0/0:2:2.51	0/0:5:3.42	0/0:5:3.42	0/0:4:3.11	0/0:6:3.72	0/0:2:2.51	0/0:1:2.21	0/0:6:3.72	0/0:4:3.11	./.	0/0:4:3.11	0/0:3:2.81	0/1:5:0.23	0/0:1:2.21	0/0:6:3.41
-1	10000179	.	C	A	4.61	.	AF=0.01;NS=60;SB=-0.47	GT:RD:GQ	0/0:3:2.66	0/0:5:3.28	0/0:4:2.95	0/0:2:2.38	./.	0/0:3:2.68	0/0:9:4.47	0/0:4:2.68	0/0:6:3.58	0/0:4:2.98	0/0:14:5.99	0/0:3:2.68	0/0:1:2.08	0/0:4:2.97	0/0:5:3.28	0/0:3:2.68	0/0:4:2.96	0/0:1:2.08	0/0:1:2.07	0/0:3:2.66	0/0:3:2.68	0/0:6:3.55	0/0:4:2.98	0/0:3:2.68	0/0:1:2.08	0/0:10:4.17	0/0:4:2.98	0/0:2:2.38	0/0:15:6.28	0/0:5:3.28	0/0:7:3.58	0/0:9:4.43	0/0:3:2.67	1/0:2:0.76	0/0:5:3.25	0/0:6:3.58	0/0:2:2.38	0/0:4:2.97	0/0:3:2.68	0/0:4:2.98	0/0:5:3.28	0/0:3:2.68	0/0:9:4.47	0/0:4:2.98	0/0:5:3.28	0/0:2:2.38	0/0:3:2.68	0/0:5:3.13	0/0:5:3.28	0/0:10:4.78	0/0:2:2.38	0/0:2:2.38	0/0:5:3.28	0/0:4:2.98	./.	0/0:4:2.98	0/0:2:2.38	0/0:5:3.27	0/0:1:2.08	0/0:3:2.68
-1	10000190	.	G	A	4.01	.	AF=0.01;NS=60;SB=-0.41	GT:RD:GQ	0/0:3:2.69	0/0:7:3.85	0/0:6:3.60	0/0:4:2.25	0/0:1:2.09	1/0:4:0.67	0/0:9:4.22	0/0:5:3.30	0/0:7:3.90	0/0:3:2.69	0/0:13:4.56	0/0:2:2.39	0/0:1:2.09	0/0:4:2.99	0/0:5:3.29	0/0:3:2.69	0/0:7:3.09	0/0:1:2.01	0/0:1:2.09	0/0:3:2.68	0/0:2:2.39	0/0:5:2.99	0/0:2:2.39	0/0:2:2.39	0/0:1:2.09	0/0:7:3.90	0/0:5:3.27	0/0:5:3.29	0/0:11:4.80	0/0:5:3.30	0/0:10:4.80	0/0:8:4.19	0/0:2:2.39	0/0:3:2.69	0/0:6:3.58	0/0:7:3.88	0/0:3:2.69	0/0:3:2.68	0/0:4:3.00	0/0:3:2.69	0/0:5:3.30	0/0:4:2.99	0/0:6:3.58	0/0:4:3.00	0/0:4:3.00	0/0:1:2.09	0/0:2:2.39	0/0:4:2.68	0/0:6:3.59	0/0:9:4.20	0/0:2:2.39	0/0:3:2.69	0/0:2:2.09	0/0:4:2.99	./.	0/0:5:3.29	0/0:4:3.00	0/0:4:2.99	0/0:4:2.92	0/0:5:3.29
-1	10000236	.	C	T	3.91	.	AF=0.01;NS=60;SB=-0.40	GT:RD:GQ	0/0:7:3.90	0/0:5:3.27	0/0:9:4.49	0/0:10:4.80	0/0:2:2.39	0/0:2:2.40	0/0:5:3.30	0/0:4:3.00	0/0:5:3.29	0/0:5:3.28	0/0:13:5.39	0/0:2:2.40	0/0:3:1.66	0/0:3:2.70	0/0:5:3.30	0/0:2:2.40	0/0:12:5.40	0/0:2:2.40	0/0:4:2.98	0/0:3:2.68	0/0:1:2.09	0/0:1:2.09	0/0:7:3.90	0/0:2:2.39	0/0:1:2.09	0/0:4:3.00	0/0:9:4.49	0/0:4:2.70	0/0:14:5.67	0/0:2:2.39	0/0:14:5.41	0/0:7:3.48	0/0:2:2.40	0/0:4:2.99	0/0:5:3.30	0/0:6:3.55	0/0:7:3.90	0/1:2:0.66	0/0:5:3.30	0/0:7:3.90	0/0:7:3.89	0/0:6:3.60	0/0:4:2.83	0/0:2:2.40	0/0:5:3.30	0/0:2:2.40	./.	0/0:4:2.85	0/0:4:3.00	0/0:4:2.99	0/0:1:1.79	0/0:5:2.40	0/0:8:3.80	0/0:5:3.30	0/0:7:3.87	0/0:6:3.60	0/0:9:3.35	0/0:6:3.60	0/0:5:3.30	0/0:3:2.70
-1	10000256	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.27	GT:RD:GQ	0/0:3:2.65	0/0:7:3.85	0/0:5:3.10	0/0:10:4.76	./.	0/0:4:2.96	0/0:4:2.96	0/0:3:2.65	0/0:4:2.92	0/0:7:3.86	0/0:17:6.55	0/0:5:3.26	0/0:2:2.23	0/0:4:2.96	0/0:3:2.66	0/0:3:2.66	0/0:8:4.16	0/0:2:2.36	0/0:4:2.96	0/0:1:2.06	0/0:3:2.66	0/0:5:3.26	0/0:7:3.75	0/0:2:2.34	0/0:1:2.06	0/0:9:4.16	0/0:4:2.96	0/0:7:3.86	0/0:14:5.97	0/0:6:3.56	0/0:11:4.58	0/0:8:4.16	0/0:3:2.66	0/0:5:3.26	0/0:7:3.86	0/0:4:2.96	0/0:6:3.18	0/0:1:2.06	0/0:5:3.26	0/0:7:3.86	0/0:6:3.56	0/0:7:3.86	0/0:11:5.07	0/0:4:2.96	0/0:1:2.06	0/0:4:2.96	0/0:1:2.06	0/0:7:3.86	0/0:5:3.26	0/0:3:2.66	0/0:2:2.36	0/0:8:4.16	0/0:7:3.73	0/0:5:3.26	0/1:2:1.10	0/0:6:3.56	0/0:4:2.96	0/0:4:2.96	0/0:2:2.36	0/0:7:3.86
-1	10000272	.	G	A	4.68	.	AF=0.01;NS=60;SB=-0.48	GT:RD:GQ	0/0:2:2.39	0/0:11:5.09	0/0:9:4.50	0/0:7:3.90	0/0:2:2.25	0/0:7:3.90	0/0:4:2.99	0/0:3:2.69	1/0:4:0.77	0/0:6:3.57	0/0:21:8.10	0/0:5:3.28	0/0:2:2.39	0/0:6:3.60	0/0:4:2.99	0/0:4:2.99	0/0:9:4.50	./.	0/0:4:2.97	0/0:3:2.66	0/0:1:2.09	0/0:10:4.79	0/0:6:3.60	0/0:8:4.18	0/0:1:2.09	0/0:6:3.59	0/0:6:2.25	0/0:6:3.60	0/0:15:6.00	0/0:6:3.57	0/0:11:4.56	0/0:12:5.37	0/0:4:2.99	0/0:2:2.39	0/0:11:4.50	0/0:3:2.68	0/0:5:2.79	0/0:2:2.39	0/0:4:2.99	0/0:4:2.99	0/0:6:3.60	0/0:3:2.69	0/0:13:3.44	0/0:6:3.60	0/0:4:2.97	0/0:6:3.60	0/0:3:2.69	0/0:7:3.88	0/0:5:3.30	0/0:4:2.25	0/0:1:2.09	0/0:11:4.88	0/0:6:3.59	0/0:4:2.99	0/0:9:4.49	0/0:5:3.29	0/0:3:2.69	0/0:5:3.28	0/0:1:2.09	0/0:6:3.59
-1	10000281	.	T	C	1.03	.	AF=0.00;NS=60;SB=-0.11	GT:RD:GQ	0/0:3:2.95	0/0:14:5.94	0/0:6:3.55	0/0:6:3.85	0/0:3:2.93	0/0:8:4.45	0/0:5:3.25	0/0:3:2.95	0/0:5:3.55	0/0:6:3.85	0/0:17:7.14	0/0:5:3.53	1/0:3:0.02	0/0:3:2.95	0/0:4:3.25	0/0:5:3.55	0/0:11:5.35	./.	0/0:4:3.24	0/0:3:2.94	0/0:2:2.50	0/0:9:4.75	0/0:7:4.15	0/0:7:3.85	0/0:1:2.34	0/0:4:3.05	0/0:9:4.48	0/0:8:4.44	0/0:14:5.65	0/0:7:4.13	0/0:10:5.05	0/0:11:5.35	0/0:3:2.95	0/0:1:2.33	0/0:9:4.75	0/0:4:3.24	0/0:3:2.94	0/0:2:2.65	0/0:4:3.25	0/0:5:3.18	0/0:4:3.25	./.	0/0:6:3.85	0/0:7:4.15	0/0:3:2.94	0/0:5:3.55	0/0:5:3.55	0/0:7:3.85	0/0:8:4.45	0/0:4:2.88	0/0:2:2.65	0/0:8:3.77	0/0:6:3.74	0/0:4:3.25	0/0:10:5.05	0/0:6:3.85	0/0:2:2.65	0/0:7:4.15	0/0:2:2.63	0/0:7:3.85
-1	10000304	.	A	T	6.19	.	AF=0.01;NS=60;SB=-0.63	GT:RD:GQ	0/0:8:4.14	0/0:13:5.68	0/0:7:3.87	0/0:3:2.67	0/0:1:1.77	0/0:10:4.76	0/0:9:4.46	0/0:1:2.07	0/0:7:3.88	0/0:7:3.88	0/0:9:4.25	0/0:4:2.97	0/0:2:2.37	0/0:2:2.37	0/0:5:3.27	0/0:5:3.28	0/0:20:7.08	0/0:3:2.63	0/0:5:3.28	0/0:4:2.97	0/0:5:3.28	0/0:5:3.28	0/0:9:4.47	0/0:5:3.28	./.	0/0:2:2.37	0/0:12:5.38	0/0:8:3.58	0/0:16:5.38	0/0:2:2.37	0/0:10:4.48	0/0:12:5.37	0/0:3:2.67	0/0:2:2.37	0/0:7:3.87	0/0:6:3.56	0/0:3:2.67	0/0:3:2.64	0/0:3:2.67	0/0:3:2.67	0/0:3:2.67	0/0:2:2.37	0/0:7:3.88	0/0:9:4.48	0/0:8:4.14	0/0:6:3.58	0/0:6:3.58	0/0:7:3.87	0/0:6:3.58	0/0:5:2.97	0/0:3:2.67	0/0:4:2.97	0/0:7:3.88	0/0:5:3.28	0/1:2:0.97	0/0:5:3.28	0/0:2:2.37	0/0:2:2.37	0/0:2:2.37	0/0:6:3.28
-1	10000390	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.53	GT:RD:GQ	0/0:2:2.12	0/0:10:4.52	0/0:12:4.82	0/0:10:4.53	0/0:5:2.72	0/0:6:3.32	0/0:10:4.53	0/0:1:1.82	0/0:8:3.91	0/0:7:3.63	0/0:14:5.67	0/0:3:1.53	1/0:4:0.47	./.	0/0:3:2.42	0/0:4:2.72	0/0:16:5.73	0/0:2:2.12	0/0:3:2.36	0/0:3:2.42	0/0:1:1.82	0/0:6:3.32	0/0:10:4.52	0/0:4:2.42	0/0:2:2.12	0/0:9:3.93	0/0:11:4.83	0/0:7:3.31	0/0:19:6.32	0/0:5:3.02	0/0:11:4.49	0/0:9:4.23	0/0:2:2.12	0/0:3:2.42	0/0:8:3.90	0/0:6:3.32	0/0:5:2.28	0/0:4:2.72	0/0:3:2.42	0/0:6:3.32	0/0:4:2.72	0/0:4:2.72	0/0:5:3.00	0/0:4:2.72	0/0:6:3.32	0/0:5:3.02	./.	0/0:5:2.79	0/0:6:3.32	0/0:5:2.78	1/0:3:0.72	0/0:3:2.42	0/0:6:3.32	0/0:4:2.72	0/0:6:3.32	0/0:6:3.32	0/0:8:3.93	0/0:7:3.32	0/0:5:3.02	0/0:9:3.63
-1	10000517	.	G	T	1.40	.	AF=0.01;NS=60;SB=-0.15	GT:RD:GQ	0/0:3:2.88	0/0:14:5.56	0/0:15:5.80	0/0:11:5.28	0/0:4:2.88	0/0:13:5.88	0/0:9:4.38	./.	0/0:6:3.78	0/0:8:4.36	0/0:20:7.69	./.	0/0:2:2.57	0/0:5:3.48	0/0:6:3.78	0/0:2:2.57	0/0:12:5.58	0/0:6:3.75	0/0:1:2.27	0/0:11:5.28	0/0:5:3.48	0/0:4:3.17	0/0:9:3.78	0/0:8:4.38	0/0:2:2.58	0/0:8:4.31	0/0:9:4.22	0/0:9:3.98	0/0:26:9.75	0/0:9:4.68	0/0:11:4.36	0/0:9:4.67	0/0:2:2.57	0/0:2:2.57	0/0:7:3.98	0/0:5:3.48	0/0:6:3.44	0/0:1:2.27	0/0:3:2.88	0/0:6:3.78	0/0:3:2.88	0/1:4:0.16	0/0:6:3.72	0/0:5:3.48	0/0:6:3.78	0/0:6:3.78	0/0:2:2.57	0/0:8:4.38	0/0:4:3.18	0/0:11:5.28	0/0:3:2.88	0/0:4:3.18	0/0:9:4.38	0/0:3:2.88	0/0:9:4.38	0/0:5:3.48	0/0:4:3.18	0/0:8:3.89	0/0:5:3.48	0/0:8:4.08
-1	10000567	.	C	A	1.19	.	AF=0.00;NS=60;SB=-2.36	GT:RD:GQ	0/0:5:3.51	0/0:7:3.75	0/0:5:3.21	0/0:7:4.10	0/0:2:2.61	0/0:5:3.51	0/0:8:4.11	0/0:2:2.59	0/0:7:4.11	0/0:4:3.20	0/0:9:4.42	0/0:5:3.49	0/0:3:2.91	0/0:6:3.78	0/0:11:5.32	0/0:3:2.91	0/0:7:3.51	0/0:1:2.31	0/0:1:2.31	0/0:4:3.19	0/0:3:2.91	0/0:5:3.51	0/0:7:4.05	0/0:7:4.12	0/0:4:3.22	0/0:8:4.41	0/0:8:4.34	0/0:4:3.21	0/0:5:3.22	0/0:3:2.91	0/0:7:3.78	0/0:8:2.55	0/0:3:2.91	0/0:1:2.31	0/0:3:2.87	0/0:6:3.81	0/0:3:2.86	0/0:2:2.59	0/0:4:3.21	0/0:5:3.51	0/0:1:2.31	1/0:4:0.03	0/0:3:2.91	0/0:8:4.35	0/0:7:3.62	0/0:9:4.68	0/0:3:2.15	0/0:1:2.31	0/0:2:2.61	0/0:6:3.50	0/0:2:2.61	0/0:1:2.31	0/0:5:3.51	0/0:3:2.91	0/0:8:4.40	0/0:6:3.82	0/0:3:0.52	0/0:5:3.48	0/0:6:3.78	0/0:4:3.21
-1	10000602	.	C	A	2.70	.	AF=0.01;NS=60;SB=-0.28	GT:RD:GQ	0/0:3:2.74	0/0:5:3.30	0/0:4:2.28	0/0:5:3.34	0/0:1:1.84	0/0:3:2.74	0/0:7:3.94	0/0:1:2.14	0/0:11:5.14	0/0:7:3.18	0/0:7:3.93	0/0:3:2.59	0/0:5:3.33	0/0:6:3.15	0/0:12:5.45	0/0:5:3.34	0/0:5:3.20	1/0:4:0.46	0/0:1:2.14	0/0:8:4.22	0/0:2:2.44	0/0:4:3.04	0/0:5:3.28	0/0:2:2.44	0/0:4:3.04	0/0:2:2.44	0/0:9:4.19	0/0:4:3.02	0/0:6:3.64	0/0:7:3.90	0/0:2:2.44	0/0:9:4.54	0/0:3:2.74	0/0:1:2.14	0/0:2:1.75	0/0:2:2.43	0/0:3:2.74	0/0:3:2.74	0/0:4:3.04	0/0:6:3.64	0/0:6:3.64	0/0:3:2.74	0/0:1:2.14	0/0:4:3.03	0/0:6:3.59	0/0:7:3.94	0/0:4:3.04	0/0:2:2.44	0/0:3:2.74	0/0:3:2.74	0/0:4:3.04	0/0:2:2.42	0/0:7:3.65	0/0:5:3.34	0/0:1:2.14	0/0:8:4.24	0/0:5:3.31	0/0:2:2.44	0/0:4:3.04	0/0:4:2.98
-1	10000635	.	C	G	0.00	.	AF=0.01;NS=60;SB=2.42	GT:RD:GQ	0/0:6:3.49	0/0:1:1.98	0/0:5:3.16	0/0:4:2.89	./.	0/0:3:2.58	0/0:5:3.19	0/0:1:1.78	0/0:5:3.18	0/0:3:2.57	0/0:7:3.79	0/0:2:2.28	0/0:1:1.98	0/0:3:2.58	0/0:11:4.99	0/0:5:3.19	0/1:2:0.96	./.	0/0:2:2.28	0/0:5:3.18	0/0:1:1.98	0/0:1:1.98	0/0:1:1.98	0/0:4:2.89	0/0:4:2.89	0/0:3:2.57	0/0:6:3.48	0/0:4:2.89	0/0:4:2.66	0/0:2:2.28	0/0:3:2.58	0/0:9:4.39	./.	0/0:1:1.98	./.	./.	0/0:1:1.98	0/0:3:2.58	0/0:4:2.89	0/0:2:2.28	0/0:1:1.98	0/0:2:2.28	./.	0/0:2:2.28	0/0:4:2.89	0/0:6:3.49	0/0:4:2.89	0/0:1:1.98	0/0:2:2.28	0/0:2:2.28	0/0:6:3.49	0/0:2:2.28	0/0:4:2.28	0/0:5:3.19	0/0:5:3.19	0/0:7:3.79	0/0:1:1.98	0/0:4:2.88	0/0:4:2.89	0/0:1:1.98
-1	10000654	.	G	A	2.72	.	AF=0.01;NS=60;SB=-0.28	GT:RD:GQ	0/0:7:3.89	0/0:8:4.15	0/0:3:2.69	0/0:2:2.39	./.	0/0:4:2.98	0/0:7:3.88	./.	0/0:3:2.69	0/0:5:3.28	0/0:7:3.87	0/0:2:2.09	./.	0/0:6:3.57	0/0:12:5.39	0/0:4:2.99	0/0:3:2.69	0/0:1:2.03	0/0:2:2.39	0/0:8:4.12	0/0:1:2.08	./.	0/0:1:2.09	0/0:3:2.69	0/0:4:2.99	0/0:3:2.39	0/0:5:2.99	0/0:3:2.69	0/0:4:2.68	0/0:4:2.99	0/0:7:3.58	0/0:9:4.41	0/0:2:2.38	0/0:1:2.09	./.	0/0:2:2.38	0/0:2:2.39	0/0:3:2.68	0/0:4:2.99	0/0:2:2.39	0/0:2:2.39	0/0:3:2.69	1/0:1:0.46	0/0:2:2.39	0/0:6:3.59	0/0:3:2.69	0/0:4:2.97	0/0:3:2.69	0/0:2:2.39	0/0:3:2.69	0/0:7:3.89	0/0:2:2.39	0/0:2:2.39	0/0:4:2.99	0/0:2:2.39	0/0:6:3.59	0/0:2:2.38	./.	0/0:4:2.60	0/0:3:2.69
-1	10000665	.	A	G	0.00	.	AF=0.01;NS=60;SB=2.48	GT:RD:GQ	0/0:6:3.55	0/0:8:4.14	0/0:3:2.34	0/1:2:0.82	./.	0/0:4:2.95	0/0:8:4.15	./.	0/0:4:2.95	0/0:6:3.55	0/0:5:3.25	0/0:2:2.34	0/0:1:2.04	0/0:6:3.55	0/0:12:5.35	0/0:4:2.95	0/0:4:2.94	0/0:2:2.34	0/0:1:2.04	0/0:11:5.05	0/0:2:2.34	./.	0/0:2:2.34	0/0:3:2.65	0/0:4:2.95	0/0:5:3.24	0/0:3:2.65	0/0:4:2.88	0/0:7:3.25	0/0:6:3.55	0/0:8:3.85	0/0:8:4.15	0/0:3:2.65	./.	0/0:1:2.04	0/0:4:2.94	0/0:3:2.65	0/0:3:2.65	0/0:4:2.95	0/0:3:2.65	0/0:2:2.34	0/0:3:2.65	0/0:1:2.04	0/0:2:2.34	0/0:4:2.95	0/0:3:2.65	0/0:2:2.34	0/0:7:3.55	0/0:2:2.34	0/0:5:3.25	0/0:6:3.55	0/0:4:2.95	0/0:3:2.41	0/0:4:2.95	0/0:1:2.04	0/0:6:3.55	0/0:1:2.04	0/0:3:2.65	0/0:3:2.65	0/0:4:2.94
-1	10000677	.	C	T	4.03	.	AF=0.01;NS=60;SB=-0.41	GT:RD:GQ	0/0:3:2.65	0/0:7:3.85	0/0:1:2.05	0/0:2:2.35	./.	0/0:5:3.23	0/0:5:3.19	0/0:1:2.05	0/0:5:3.25	0/0:3:2.65	0/0:3:2.65	0/0:1:2.04	0/0:1:2.05	0/0:7:3.83	0/0:11:5.05	0/0:4:2.95	0/0:6:3.05	0/0:1:2.05	0/0:2:2.33	0/0:10:4.68	0/0:2:2.05	./.	0/0:1:2.05	0/0:2:2.35	0/0:4:2.95	0/0:5:3.25	0/0:1:2.05	0/0:3:2.61	0/0:10:4.45	0/0:6:3.53	0/0:4:2.52	0/0:4:2.95	0/0:4:2.95	./.	0/0:2:2.35	0/0:5:3.09	0/0:1:2.04	0/0:3:2.65	0/1:4:0.67	0/0:3:2.65	0/0:3:2.64	0/0:2:2.35	0/0:1:2.05	0/0:2:2.30	0/0:3:2.61	0/0:4:2.95	0/0:3:2.65	0/0:7:3.85	0/0:3:2.65	0/0:7:3.85	0/0:6:3.55	0/0:4:2.95	0/0:3:2.57	0/0:2:2.35	./.	0/0:7:3.85	0/0:1:2.05	0/0:3:2.52	0/0:3:2.64	0/0:1:2.05
-1	10000700	.	T	C	2.21	.	AF=0.01;NS=60;SB=-0.23	GT:RD:GQ	0/0:1:2.06	0/0:8:4.16	./.	0/0:5:3.23	0/0:1:2.06	0/0:2:2.36	0/0:3:2.66	1/0:1:0.36	0/0:4:2.96	0/0:1:2.06	0/0:3:2.66	0/0:2:1.84	0/0:1:2.06	0/0:6:3.55	0/0:7:3.86	0/0:4:2.96	0/0:5:3.23	./.	0/0:2:2.36	0/0:4:2.96	0/0:1:2.05	0/0:2:2.34	./.	0/0:2:2.36	0/0:2:2.35	0/0:4:2.72	./.	0/0:2:2.36	0/0:6:3.45	0/0:3:2.66	0/0:6:3.54	0/0:4:2.96	0/0:1:2.06	./.	./.	0/0:1:1.54	0/0:1:2.06	0/0:3:2.66	0/0:4:2.96	0/0:3:2.65	0/0:4:2.96	./.	0/0:1:2.06	0/0:2:2.36	0/0:1:2.06	0/0:5:3.26	0/0:2:2.27	0/0:2:2.30	0/0:2:2.36	0/0:3:2.66	0/0:6:3.56	0/0:1:2.06	0/0:1:1.83	0/0:2:2.36	0/0:2:2.06	0/0:7:3.86	0/0:3:2.66	0/0:3:2.66	0/0:4:2.95	0/0:1:2.06
-1	10000708	.	C	T	0.00	.	AF=0.03;NS=60;SB=-0.83	GT:RD:GQ	0/0:1:1.59	0/0:9:3.97	./.	0/0:4:2.49	0/0:1:1.59	0/0:2:1.89	0/0:1:1.59	0/0:1:1.59	0/0:2:1.89	0/0:1:1.59	0/0:2:1.89	0/0:1:1.59	0/0:1:1.59	0/1:5:1.22	0/0:7:3.38	0/0:4:2.48	0/0:4:2.48	./.	0/0:2:1.89	0/0:2:1.89	0/0:1:1.58	0/0:2:1.85	0/0:1:1.59	0/0:2:1.89	0/0:2:1.89	0/0:2:1.89	./.	0/0:1:1.59	0/0:7:3.35	0/0:2:1.89	0/0:7:3.39	0/0:3:2.19	./.	./.	./.	./.	0/0:1:1.57	0/0:3:2.17	0/0:3:2.19	0/0:1:1.59	0/0:4:2.49	./.	0/0:1:1.59	0/0:2:1.89	0/0:2:1.89	0/0:3:2.19	0/0:1:1.59	0/0:1:1.59	0/0:3:2.19	0/0:4:2.49	0/0:6:3.08	0/0:2:1.89	0/1:2:1.52	0/0:2:1.88	0/0:3:2.19	0/0:6:3.08	0/0:2:1.89	0/0:3:2.19	0/0:6:3.08	0/0:1:1.59
-1	10000728	.	A	C	0.00	.	AF=0.02;NS=60;SB=2.53	GT:RD:GQ	0/0:1:1.77	0/0:6:2.08	0/0:1:1.77	0/0:2:2.08	0/0:1:1.77	0/0:1:1.77	./.	0/0:2:2.08	0/0:3:2.38	0/0:1:1.77	0/0:1:1.77	0/0:1:1.77	0/0:1:1.77	0/1:5:1.03	0/0:7:3.58	0/0:4:2.68	0/0:4:2.44	./.	0/0:1:1.77	0/0:2:2.08	0/0:1:1.77	0/0:1:1.77	0/0:1:1.77	0/0:4:2.68	0/0:2:2.08	0/0:3:2.38	0/0:4:2.68	0/0:1:1.77	0/0:4:2.68	0/0:2:2.08	0/0:2:2.07	0/0:7:3.57	./.	0/0:1:1.77	0/0:1:1.77	0/0:1:1.76	0/0:2:1.98	0/0:5:2.98	0/0:3:2.38	0/0:1:1.77	0/0:2:2.08	./.	./.	0/0:1:1.77	0/0:2:2.07	0/0:3:2.38	./.	./.	0/0:2:2.08	0/0:2:1.77	0/0:6:0.32	0/0:1:1.77	0/0:1:1.77	0/0:3:2.38	0/0:1:1.77	0/0:7:3.58	0/0:1:1.77	0/0:4:2.64	0/0:5:2.98	0/0:1:1.77
-1	10000730	.	A	G	2.11	.	AF=0.01;NS=60;SB=-0.22	GT:RD:GQ	0/0:1:2.01	0/0:6:2.99	0/0:2:2.32	0/0:2:2.31	0/0:1:2.01	0/0:2:2.30	./.	0/0:2:2.32	0/0:3:2.62	0/0:1:2.01	./.	0/0:2:2.30	0/0:1:2.01	0/1:5:0.34	0/0:7:3.82	0/0:4:2.91	0/0:4:2.49	./.	0/0:1:2.01	0/0:2:2.32	0/0:1:2.01	0/0:1:2.01	0/0:1:1.71	0/0:5:2.81	0/0:2:2.01	0/0:4:2.92	0/0:4:2.72	0/0:1:2.00	0/0:5:2.91	0/0:2:2.31	0/0:3:2.31	0/0:8:4.12	./.	0/0:1:2.01	0/0:1:2.01	0/0:1:1.50	0/0:2:2.08	0/0:5:3.22	0/0:3:2.62	0/0:1:2.01	0/0:2:2.32	./.	./.	0/0:2:2.32	0/0:2:2.19	0/0:3:2.62	./.	./.	0/0:3:2.62	0/0:2:2.31	0/0:6:3.52	0/0:1:2.01	./.	0/0:3:2.62	./.	0/0:7:3.82	0/0:1:2.01	0/0:4:2.86	0/0:5:3.22	0/0:1:2.01
-1	10000734	.	G	A	0.00	.	AF=0.01;NS=60;SB=2.19	GT:RD:GQ	0/0:2:2.17	0/0:6:3.32	0/0:2:2.17	./.	0/0:1:1.87	0/0:2:2.17	./.	0/0:2:1.57	0/0:3:2.47	0/0:1:1.87	./.	0/0:2:2.11	0/0:1:1.87	0/0:6:3.37	0/0:7:3.67	0/0:4:2.77	0/0:5:2.75	./.	0/0:1:1.87	0/0:2:2.17	0/0:3:2.47	./.	./.	0/0:5:3.08	0/0:2:2.17	0/0:5:3.06	0/0:5:3.07	0/0:1:1.86	0/0:5:3.08	0/0:2:2.17	0/0:2:2.17	0/0:9:4.18	./.	0/0:1:1.87	0/0:2:2.17	0/0:1:1.85	0/0:2:2.03	0/0:5:3.08	0/0:3:2.47	0/0:1:1.87	0/0:1:1.87	./.	./.	0/0:1:1.87	0/0:3:2.47	1/0:3:1.30	0/0:1:1.87	0/0:1:1.85	0/0:3:2.47	0/0:2:1.65	0/0:6:3.37	0/0:1:1.87	./.	0/0:3:2.47	./.	0/0:6:3.37	0/0:1:1.87	0/0:4:2.76	0/0:5:3.07	0/0:1:1.87
-1	10000736	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.39	GT:RD:GQ	0/0:2:2.20	0/0:6:3.38	0/0:3:2.19	./.	0/0:2:1.89	0/0:2:2.19	./.	./.	0/0:3:2.50	0/0:1:1.89	./.	0/0:2:2.07	0/0:2:2.19	0/0:6:3.27	0/0:7:3.70	0/0:4:2.80	0/0:4:2.79	0/0:1:1.59	0/0:1:1.89	0/0:2:2.18	0/0:3:2.50	./.	./.	0/0:5:3.10	0/0:2:2.20	0/0:5:3.10	0/0:5:3.09	0/0:1:1.89	0/0:4:2.79	0/0:2:2.19	0/0:2:2.20	0/0:9:4.29	./.	0/0:1:1.89	0/0:2:2.19	0/0:1:1.88	0/0:1:1.89	0/0:5:3.10	0/0:3:2.50	0/0:1:1.89	0/0:1:1.89	./.	./.	0/0:1:1.89	0/0:3:2.37	1/0:3:1.05	0/0:1:1.89	0/0:1:1.89	0/0:3:2.50	0/0:2:1.83	0/0:6:3.40	0/0:1:1.89	./.	0/0:3:2.50	./.	0/0:6:3.40	0/0:1:1.89	0/0:5:2.79	0/0:5:3.09	0/0:1:1.89
-1	10000737	.	G	A	0.00	.	AF=0.01;NS=60;SB=2.20	GT:RD:GQ	0/0:2:2.19	0/0:6:3.21	0/0:2:2.19	./.	0/0:2:2.19	0/0:2:2.19	./.	./.	0/0:3:2.49	0/0:2:2.19	./.	0/0:2:2.19	0/0:2:2.19	0/0:5:3.09	0/0:7:3.69	0/0:4:2.79	0/0:4:2.79	0/0:1:1.89	0/0:1:1.89	0/0:2:2.19	0/0:3:2.49	./.	./.	0/0:5:3.09	0/0:2:2.19	0/0:4:2.78	0/0:6:3.39	0/0:1:1.88	0/0:4:2.49	0/0:2:2.19	0/0:2:2.19	0/0:8:3.96	./.	0/0:1:1.89	0/0:2:2.17	0/0:1:1.73	0/0:1:1.89	0/0:5:3.09	0/0:3:2.49	0/0:1:1.89	0/0:1:1.89	./.	./.	0/0:1:1.89	0/0:3:2.49	1/0:3:1.28	0/0:1:1.89	0/0:1:1.88	0/0:3:2.49	0/0:2:1.89	0/0:6:3.39	0/0:2:2.19	./.	0/0:3:2.49	./.	0/0:6:3.39	0/0:1:1.89	0/0:5:3.07	0/0:5:3.09	0/0:1:1.89
-1	10000739	.	A	G	0.00	.	AF=0.05;NS=60;SB=0.22	GT:RD:GQ	0/0:2:1.60	0/0:6:2.78	0/0:3:1.60	./.	0/0:2:1.60	0/0:2:1.59	./.	./.	0/0:3:1.90	0/0:2:1.59	./.	0/0:2:1.56	0/0:2:1.60	0/1:5:1.05	0/0:7:3.10	0/0:4:2.20	0/0:4:2.18	0/0:1:1.30	0/0:1:1.30	0/0:2:1.60	0/0:3:1.90	./.	0/0:1:0.99	0/0:4:2.20	0/0:2:1.60	0/0:4:1.88	0/0:6:2.49	0/0:2:1.60	0/0:3:1.89	0/0:2:1.60	0/0:2:1.60	0/0:8:3.39	./.	0/0:1:1.30	0/0:2:1.30	0/0:1:0.78	0/0:2:0.82	0/0:5:2.50	0/0:3:1.90	./.	0/0:1:1.30	./.	./.	0/0:1:1.30	0/0:3:1.90	0/1:3:1.55	0/0:1:1.29	0/0:1:1.29	0/0:3:1.90	0/0:1:1.30	0/1:6:0.34	0/0:2:1.60	./.	0/0:3:1.90	./.	0/1:6:0.54	0/0:1:1.30	0/0:5:2.40	0/0:4:2.16	0/0:1:1.30
-1	10000740	.	C	T	0.00	.	AF=0.01;NS=60;SB=-0.21	GT:RD:GQ	0/0:2:2.18	0/1:6:1.51	0/0:3:2.48	./.	0/0:2:2.18	0/0:2:2.17	./.	./.	0/0:3:2.48	0/0:2:2.14	./.	0/0:2:2.17	0/0:2:2.18	0/0:5:3.09	0/0:7:3.68	0/0:4:2.79	0/0:4:2.79	0/0:1:1.88	0/0:1:1.88	0/0:2:2.18	0/0:3:2.48	./.	0/0:1:1.88	0/0:4:2.79	0/0:2:2.18	0/0:5:3.07	0/0:5:3.08	0/0:2:2.18	0/0:3:2.48	0/0:2:2.18	0/0:1:1.88	0/0:8:3.98	./.	0/0:1:1.88	0/0:1:1.88	0/0:1:1.88	0/0:2:2.16	0/0:5:3.08	0/0:3:2.48	./.	0/0:1:1.88	./.	./.	0/0:1:1.88	0/0:3:2.48	0/0:3:2.48	0/0:1:1.88	0/0:1:1.85	0/0:3:2.48	0/0:1:1.88	0/0:6:3.38	0/0:2:2.18	./.	0/0:3:2.48	./.	0/0:6:3.38	0/0:1:1.88	0/0:5:2.98	0/0:4:2.79	0/0:1:1.88
-1	10000745	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.48	GT:RD:GQ	0/0:2:2.22	0/0:5:3.11	0/0:3:2.52	./.	0/0:1:1.92	0/0:2:2.21	./.	./.	0/0:4:2.80	0/0:2:2.22	./.	0/0:2:2.18	0/0:2:2.20	0/0:6:3.42	0/0:7:3.72	0/0:5:3.12	0/0:6:3.42	0/0:1:1.92	0/0:1:1.92	0/0:2:2.22	0/0:3:2.52	./.	0/0:1:1.92	0/0:5:3.12	0/0:2:2.22	0/0:7:3.72	0/0:6:2.11	0/0:2:2.21	0/0:4:2.71	0/0:2:2.22	0/0:1:1.92	0/0:8:4.01	./.	0/0:1:1.92	0/0:2:2.22	0/0:1:1.92	0/0:2:2.19	0/0:5:3.12	0/0:3:2.52	./.	0/0:1:1.92	./.	./.	0/0:1:1.40	0/0:4:2.82	1/0:3:0.92	0/0:2:2.21	0/0:2:2.21	0/0:4:2.82	0/0:2:1.92	0/0:6:3.42	0/0:2:2.20	0/0:1:1.62	0/0:3:2.52	./.	0/0:6:3.42	0/0:1:1.92	0/0:5:3.09	0/0:3:2.39	0/0:1:1.92
-1	10000748	.	T	C	0.00	.	AF=0.02;NS=60;SB=2.32	GT:RD:GQ	0/0:2:1.18	0/0:6:3.13	0/0:3:2.24	./.	0/0:1:1.63	0/0:2:1.89	./.	./.	0/0:4:2.50	0/0:1:1.63	./.	0/0:2:1.93	0/0:2:1.93	1/0:6:0.30	0/0:7:3.44	0/0:5:2.84	0/0:7:2.84	0/0:1:1.63	0/0:1:1.63	0/0:3:2.20	0/0:3:2.24	./.	0/0:1:1.63	0/0:5:2.84	0/0:2:1.94	0/0:7:2.97	0/0:6:2.57	0/0:2:1.93	0/0:4:2.54	0/0:2:1.94	0/0:1:1.63	0/0:9:4.00	./.	0/0:1:1.63	0/0:2:1.94	0/0:1:1.63	0/0:2:1.80	0/0:5:2.84	0/0:2:1.94	./.	0/0:1:1.63	./.	./.	0/0:2:1.93	0/0:5:2.84	1/0:3:1.21	0/0:2:1.80	0/0:2:1.93	0/0:3:2.24	0/0:2:1.94	0/0:6:3.14	0/0:2:1.93	0/0:1:1.63	0/0:3:2.24	./.	0/0:6:3.14	0/0:2:1.94	0/0:5:2.82	0/0:3:0.68	0/0:1:1.63
-1	10000750	.	G	A,C,T	0.00	.	AF=0.03;NS=60;SB=0.90	GT:RD:GQ	0/0:2:1.78	0/0:5:1.18	0/0:3:2.08	./.	0/0:1:1.47	0/0:2:1.78	./.	./.	0/0:3:2.07	0/0:1:1.47	./.	0/0:2:1.77	0/0:2:1.78	1/0:6:0.16	0/0:7:3.28	0/0:5:2.68	0/0:5:2.68	0/0:1:1.47	0/0:1:1.47	0/0:3:1.72	0/0:3:2.07	./.	0/0:1:1.47	2/0:6:0.24	0/0:2:1.78	0/0:7:3.28	0/0:7:1.59	0/0:1:1.47	0/0:4:2.15	0/0:2:1.78	0/0:1:1.47	0/0:9:3.85	./.	0/0:1:1.47	0/0:2:1.67	0/0:1:1.47	0/0:2:0.82	0/0:6:2.98	0/0:2:1.78	./.	0/0:1:1.47	./.	./.	0/0:2:1.77	0/0:5:2.68	2/0:3:2.30	0/0:2:1.78	0/0:2:1.77	0/0:3:2.08	0/0:2:1.78	0/3:6:0.19	0/0:2:1.77	0/0:2:1.77	0/0:3:2.08	./.	2/0:6:0.50	0/0:2:1.78	0/0:5:2.67	0/0:4:2.37	0/0:1:1.47
-1	10000752	.	C	T	0.00	.	AF=0.02;NS=60;SB=-0.15	GT:RD:GQ	0/0:2:1.94	0/0:5:2.80	0/0:3:2.24	./.	0/0:1:1.64	0/0:2:1.84	./.	0/0:1:1.34	0/0:3:0.98	0/0:1:1.64	0/0:2:1.34	0/0:2:1.86	0/0:2:1.91	0/0:6:3.13	0/0:7:3.43	0/0:5:2.84	0/0:5:2.84	0/0:1:1.64	0/0:1:1.64	0/0:3:2.10	0/0:3:2.24	./.	0/0:1:1.64	0/0:5:2.84	0/0:2:1.94	0/0:7:3.40	0/0:7:3.35	0/0:1:1.64	0/0:4:2.53	0/0:2:1.94	0/0:1:1.64	0/0:10:4.29	./.	0/0:1:1.64	0/0:2:1.94	0/0:1:1.64	0/0:1:1.63	0/0:6:3.14	0/0:2:1.94	./.	0/0:1:1.64	./.	./.	0/0:2:1.94	0/0:5:2.69	0/1:3:1.48	0/0:2:1.93	0/0:2:1.91	0/0:3:2.23	0/0:2:1.94	0/0:6:3.14	0/0:2:1.83	0/0:2:1.91	0/0:3:2.24	./.	0/1:6:0.33	0/0:1:1.64	0/0:5:2.81	0/0:3:2.24	0/0:1:1.64
-1	10000753	.	G	A	1.23	.	AF=0.01;NS=60;SB=-0.11	GT:RD:GQ	0/0:2:2.46	0/0:5:3.19	0/0:3:2.47	./.	0/0:1:2.16	0/0:2:2.38	./.	0/0:1:2.16	0/0:3:2.58	0/0:1:2.16	0/0:2:2.47	0/0:2:2.12	0/0:2:2.46	1/0:6:0.10	0/0:7:3.95	0/0:5:3.37	0/0:5:3.37	0/0:1:2.16	0/0:1:2.16	0/0:3:2.72	0/0:3:2.77	./.	0/0:1:2.16	0/0:5:3.06	0/0:2:2.45	0/0:7:3.97	0/0:8:4.02	0/0:1:2.16	0/0:4:3.07	0/0:2:2.46	0/0:1:2.16	0/0:10:4.84	./.	0/0:1:2.16	0/0:2:2.47	0/0:1:2.16	0/0:1:2.16	0/0:6:3.67	0/0:2:2.46	./.	0/0:1:2.16	./.	./.	0/0:2:2.46	0/0:5:3.22	0/0:3:2.76	0/0:2:2.46	0/0:2:2.45	0/0:3:2.76	0/0:2:2.46	0/0:6:3.67	0/0:2:2.45	0/0:2:2.47	0/0:4:3.06	./.	0/0:6:3.66	0/0:1:2.16	0/0:5:3.33	0/0:4:2.89	0/0:1:2.16
-1	10000755	.	C	A	0.00	.	AF=0.01;NS=60;SB=1.97	GT:RD:GQ	0/0:2:2.20	0/0:4:2.31	0/0:2:2.20	./.	0/0:1:1.90	0/0:2:2.20	./.	0/0:1:1.90	0/0:4:2.80	0/0:2:2.20	0/0:2:2.20	0/0:2:2.19	0/0:2:2.20	0/0:6:3.40	0/0:7:3.71	0/0:5:3.10	0/0:6:3.06	0/0:1:1.90	0/0:1:1.90	0/0:3:2.50	0/0:3:2.50	./.	0/0:1:1.90	0/0:4:2.80	0/0:2:2.20	0/0:6:3.40	0/0:8:3.47	0/0:1:1.88	0/0:4:2.66	0/0:2:2.20	0/0:1:1.90	0/0:9:4.30	./.	0/0:1:1.90	0/0:2:1.83	0/0:1:1.90	0/0:1:1.90	0/0:6:3.41	0/0:1:1.90	./.	0/0:1:1.90	./.	./.	0/0:2:2.20	0/0:5:3.02	1/0:3:1.53	0/0:2:2.20	0/0:2:2.17	0/0:4:2.80	0/0:2:2.20	0/0:6:3.40	0/0:2:2.07	0/0:2:2.05	0/0:4:2.80	./.	0/0:6:3.41	0/0:1:1.90	0/0:5:3.10	0/0:3:2.46	./.
-1	10000759	.	A	G	0.00	.	AF=0.01;NS=60;SB=2.49	GT:RD:GQ	0/0:2:2.22	0/0:4:2.82	0/0:2:1.92	0/0:1:1.92	0/0:1:1.92	0/0:2:2.22	./.	0/0:1:1.92	0/0:4:2.80	0/0:2:2.22	0/0:2:2.22	0/0:2:1.99	0/0:2:2.22	0/0:6:3.43	0/0:7:3.72	0/0:5:3.13	0/0:6:3.42	0/0:1:1.92	0/0:1:1.92	0/0:3:2.49	0/0:2:2.22	./.	0/0:1:1.92	0/0:5:2.83	0/0:2:2.22	0/0:7:3.34	0/0:7:3.49	0/0:1:1.92	0/0:3:2.51	0/0:2:2.22	0/0:1:1.92	0/0:9:4.32	./.	0/0:1:1.80	0/0:2:2.22	0/0:1:1.92	0/0:1:1.34	0/0:6:3.43	0/0:1:1.92	./.	0/0:1:1.92	./.	./.	0/0:2:2.22	0/0:5:3.11	0/1:3:0.92	0/0:2:2.22	0/0:1:1.92	0/0:4:2.82	0/0:2:2.22	0/0:6:3.43	0/0:1:1.92	0/0:2:1.89	0/0:4:2.83	./.	0/0:6:3.43	0/0:1:1.92	0/0:4:2.82	0/0:3:2.52	./.
-1	10000760	.	G	A	0.00	.	AF=0.02;NS=60;SB=0.33	GT:RD:GQ	0/0:2:1.94	0/0:4:2.51	0/0:1:1.64	0/0:1:1.64	0/0:1:1.34	0/0:2:1.94	./.	0/0:1:1.64	0/0:4:2.30	0/0:2:1.94	0/0:2:1.80	0/0:2:1.91	0/0:2:1.93	1/0:5:1.02	0/0:6:3.14	0/0:5:2.84	0/0:6:3.15	0/0:1:1.34	0/0:1:1.64	0/0:2:1.93	0/0:2:1.94	./.	0/0:1:1.64	0/0:5:2.84	0/0:2:1.94	0/0:7:3.44	0/0:7:3.43	0/0:1:1.64	0/0:2:1.93	0/0:2:1.94	0/0:1:1.64	0/0:9:4.00	./.	0/0:1:1.64	0/0:2:1.94	0/0:1:1.64	0/0:1:1.64	0/0:6:3.15	0/0:1:1.64	./.	0/0:1:1.64	./.	./.	0/0:2:1.94	0/0:5:2.84	0/0:3:2.24	0/0:2:1.94	0/0:1:1.64	0/0:4:2.45	0/0:2:1.94	0/0:6:3.14	0/0:1:1.64	0/0:2:1.47	0/0:4:2.54	0/0:1:1.34	1/0:6:0.48	0/0:1:1.64	0/0:5:2.54	0/0:3:2.24	./.
-1	10000762	.	C	T	0.00	.	AF=0.02;NS=60;SB=1.47	GT:RD:GQ	0/0:2:1.88	0/0:4:2.48	0/0:1:1.59	0/0:1:1.59	./.	0/0:2:1.89	./.	0/0:1:1.59	0/0:4:2.44	0/0:2:1.89	0/0:2:1.89	0/0:2:1.73	0/0:2:1.88	0/0:5:2.79	0/0:6:3.09	0/0:5:2.79	0/0:6:3.09	./.	0/0:1:1.59	0/0:2:1.89	0/0:2:1.88	./.	0/0:1:1.59	0/0:5:2.79	0/0:2:1.89	0/1:6:1.26	0/0:7:3.38	0/0:1:1.59	0/0:2:1.89	0/0:2:1.89	0/0:2:1.59	0/0:8:3.67	./.	0/1:1:1.46	0/0:2:1.89	0/0:1:1.59	0/0:1:1.59	0/0:6:3.10	0/0:1:1.59	./.	0/0:1:1.59	./.	./.	0/0:2:1.89	0/0:5:2.79	0/0:3:2.19	0/0:2:1.85	0/0:1:1.59	0/0:4:2.49	0/0:2:1.89	0/0:6:3.09	0/0:1:1.59	0/0:3:2.19	0/0:4:2.49	0/0:1:1.59	0/0:6:3.09	0/0:1:1.59	0/0:4:2.49	0/0:3:2.19	./.
-1	10000763	.	C	T	1.98	.	AF=0.01;NS=60;SB=-0.21	GT:RD:GQ	0/0:2:2.35	0/0:4:1.83	0/0:1:1.76	0/0:2:2.36	./.	0/0:2:2.36	./.	0/0:1:2.06	0/0:5:3.25	0/0:2:2.36	0/0:2:2.36	0/0:2:2.35	0/0:2:2.36	0/0:5:3.26	0/0:6:3.56	0/0:5:3.26	0/0:6:3.56	./.	0/0:1:2.06	0/0:2:2.35	0/0:2:2.36	./.	0/0:1:1.76	0/1:5:0.30	0/0:2:2.36	0/0:6:3.23	0/0:7:3.85	0/0:1:2.06	0/0:2:2.36	0/0:2:2.36	0/0:2:2.35	0/0:8:4.16	./.	0/0:1:2.06	0/0:2:2.36	0/0:1:2.06	0/0:1:2.06	0/0:6:3.56	0/0:1:2.06	./.	0/0:1:2.06	./.	./.	0/0:2:2.36	0/0:5:3.07	0/0:3:2.66	0/0:2:2.36	0/0:1:2.06	0/0:4:2.96	0/0:2:2.36	0/0:6:3.56	0/0:1:2.06	0/0:3:2.66	0/0:4:2.96	0/0:1:2.06	0/0:6:3.56	0/0:1:2.06	0/0:4:2.96	0/0:3:2.66	./.
-1	10000767	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.45	GT:RD:GQ	0/0:2:2.19	0/0:3:2.50	./.	0/0:2:2.20	./.	0/0:2:2.20	./.	0/0:2:1.99	0/0:4:2.73	0/0:2:2.20	0/0:2:2.20	0/0:2:1.31	0/1:2:0.97	0/0:5:3.10	0/0:6:3.40	0/0:5:3.10	0/0:6:3.10	./.	0/0:2:1.80	0/0:2:2.20	0/0:2:2.16	./.	./.	0/0:4:2.80	0/0:2:2.20	0/0:6:3.38	0/0:6:2.37	0/0:2:1.90	0/0:1:1.90	0/0:2:2.20	0/0:3:2.19	0/0:8:4.00	./.	./.	0/0:1:1.90	0/0:1:1.90	0/0:1:1.90	0/0:6:3.41	0/0:1:1.90	./.	0/0:1:1.90	./.	./.	0/0:2:2.20	0/0:5:3.01	0/0:3:2.50	0/0:2:2.16	0/0:2:2.20	0/0:5:3.10	0/0:2:2.20	0/0:6:3.40	0/0:1:1.90	0/0:3:2.50	0/0:4:2.80	0/0:1:1.90	0/0:6:3.40	0/0:1:1.90	0/0:4:2.80	0/0:3:2.50	0/0:1:1.90
-1	10000773	.	A	T	0.00	.	AF=0.02;NS=60;SB=2.63	GT:RD:GQ	0/0:1:1.67	0/0:3:2.27	./.	0/0:2:1.97	./.	0/0:1:1.67	./.	0/0:2:1.91	0/0:3:2.27	0/0:2:1.97	0/0:2:1.97	0/0:2:1.94	0/0:1:1.67	0/0:5:1.78	0/0:6:3.17	0/0:5:2.87	0/0:5:2.86	0/0:2:1.97	0/0:3:2.27	0/0:5:2.87	0/0:3:1.63	./.	./.	0/0:4:2.57	0/0:1:1.67	0/0:6:3.16	0/0:6:3.12	0/0:2:1.97	0/0:1:1.67	0/0:2:1.97	0/0:3:1.86	0/0:8:3.76	./.	./.	0/0:1:1.67	0/0:1:1.67	0/0:1:1.67	0/0:6:3.17	0/0:1:1.67	./.	0/0:1:1.67	0/0:1:1.67	./.	0/0:2:1.95	0/0:6:3.14	0/0:4:2.57	0/0:2:1.56	0/0:2:1.97	0/0:5:2.87	0/0:1:1.67	0/0:6:1.28	0/0:1:1.66	0/0:2:1.67	0/1:5:0.59	0/0:1:1.67	0/1:6:0.59	0/0:1:1.67	0/0:4:2.56	0/0:3:2.27	0/0:1:1.67
-1	10000780	.	T	A	0.00	.	AF=0.01;NS=60;SB=2.80	GT:RD:GQ	0/0:1:1.88	0/0:2:2.16	./.	0/0:3:2.48	./.	0/0:1:1.88	./.	0/0:1:1.88	0/0:4:2.78	0/0:2:2.17	./.	0/0:1:0.54	0/0:1:1.88	0/0:5:3.08	0/0:5:3.08	0/0:6:3.38	0/0:3:2.48	0/0:2:2.18	0/0:3:2.48	0/0:6:3.38	0/0:2:2.00	./.	./.	0/0:3:2.48	0/0:1:1.88	0/0:4:2.78	0/0:5:3.08	0/0:1:1.88	0/0:1:1.88	0/0:2:2.18	0/0:3:2.48	0/0:5:3.08	./.	./.	0/0:2:1.88	./.	0/0:1:1.88	0/0:6:3.38	0/0:1:1.88	./.	0/0:1:1.88	0/0:1:1.88	0/0:1:1.88	0/0:2:2.17	0/0:6:3.16	0/0:4:2.78	0/0:2:2.00	0/0:2:2.18	0/0:4:2.78	0/0:1:1.88	0/0:6:3.38	0/0:1:1.88	0/0:1:1.88	1/0:5:0.48	0/0:1:1.88	0/0:7:3.68	0/0:1:1.88	0/0:1:1.88	0/0:3:2.48	0/0:1:1.88
-1	10000785	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.01	GT:RD:GQ	0/0:1:1.85	0/0:2:2.15	./.	0/0:3:2.44	./.	0/0:1:1.85	./.	0/0:1:1.85	0/0:4:2.75	0/0:2:2.14	./.	./.	0/0:1:1.85	0/0:5:3.05	0/0:5:3.05	0/0:6:3.35	0/0:2:2.15	0/0:2:2.15	0/0:4:2.35	0/0:6:3.35	0/0:1:1.85	./.	0/0:1:1.85	0/0:2:2.15	0/0:1:1.85	0/0:3:2.45	0/0:6:3.35	0/0:1:1.85	0/0:1:1.85	0/0:2:2.15	0/0:3:2.42	0/0:2:2.14	./.	./.	0/0:1:1.85	./.	0/0:1:1.85	0/0:6:3.35	0/0:1:1.85	./.	0/0:2:2.15	0/0:2:2.15	0/1:1:1.52	0/0:1:1.85	0/0:5:2.92	0/0:3:2.45	0/0:1:1.85	0/0:2:2.15	0/0:5:2.97	0/0:2:2.11	0/0:6:3.35	0/0:1:1.55	0/0:1:1.85	0/0:5:3.05	./.	0/0:7:3.65	./.	0/0:1:1.85	0/0:3:2.45	0/0:3:2.45
-1	10000798	.	T	C	1.34	.	AF=0.01;NS=60;SB=-0.14	GT:RD:GQ	0/0:1:2.10	0/0:3:2.70	0/0:1:2.10	0/0:4:3.00	./.	0/0:2:2.40	./.	./.	0/0:4:3.00	0/0:2:2.40	0/0:1:2.10	./.	./.	1/0:5:0.14	0/0:4:3.00	0/0:6:3.61	0/0:3:2.70	0/0:1:2.10	0/0:5:3.31	0/0:7:3.91	./.	0/0:1:2.10	0/0:1:2.10	0/0:3:2.70	0/0:1:2.10	0/0:3:2.70	0/0:4:3.00	0/0:2:2.40	0/0:2:2.40	0/0:2:2.10	0/0:2:2.15	0/0:3:2.70	./.	./.	0/0:1:2.10	0/0:1:2.10	0/0:2:2.40	0/0:6:3.61	0/0:3:2.70	./.	0/0:2:2.40	0/0:3:2.70	0/0:2:2.40	./.	0/0:2:2.40	0/0:3:2.70	./.	0/0:2:2.40	0/0:6:3.60	0/0:2:2.39	0/0:6:3.61	./.	./.	0/0:4:3.00	./.	0/0:5:3.30	0/0:1:2.10	0/0:2:2.40	0/0:3:2.70	0/0:4:3.00
-1	10000802	.	C	A,G	0.00	.	AF=0.01;NS=60;SB=2.46	GT:RD:GQ	0/0:1:1.88	0/0:4:0.73	0/0:1:1.88	0/0:4:2.78	./.	0/0:2:2.18	./.	0/0:1:1.76	0/0:4:2.77	0/0:2:2.18	0/0:1:1.88	./.	./.	0/0:5:3.08	0/0:4:2.78	0/0:6:3.39	0/0:3:2.48	0/0:1:1.88	0/0:5:3.08	0/0:6:3.38	./.	0/0:1:1.88	0/0:1:1.88	0/0:3:2.48	0/0:1:1.88	0/0:3:2.48	0/0:4:2.42	0/0:2:2.18	0/0:2:2.18	0/0:2:2.18	0/0:1:1.88	0/0:2:2.18	./.	./.	0/0:1:1.88	0/0:1:1.88	0/0:2:2.18	0/0:7:3.69	0/0:3:2.48	./.	0/0:2:2.18	0/0:3:2.48	0/0:1:1.88	./.	0/0:1:1.88	0/0:3:2.48	./.	0/0:2:2.18	0/0:6:3.39	1/0:2:0.12	0/0:6:3.39	./.	./.	0/0:4:2.78	./.	0/2:5:0.99	0/0:1:1.88	0/0:2:2.18	0/0:3:2.48	0/0:3:2.48
-1	10000805	.	A	G,T	0.00	.	AF=0.01;NS=60;SB=0.57	GT:RD:GQ	0/0:1:1.90	0/0:4:2.46	0/0:1:1.90	0/0:4:2.80	./.	0/0:2:2.20	./.	0/0:1:1.79	0/0:3:2.50	0/0:2:2.20	0/0:1:1.90	./.	./.	0/0:5:3.10	0/0:4:2.80	0/0:6:3.40	0/0:3:2.50	0/0:1:1.90	0/0:5:3.10	0/0:6:3.40	./.	0/0:1:1.90	0/0:1:1.90	0/0:2:2.20	0/0:1:1.90	0/0:3:2.50	0/0:3:2.50	0/0:2:2.09	0/0:1:1.90	0/0:2:2.20	0/0:2:2.19	0/0:1:1.90	./.	./.	./.	0/0:2:2.19	0/0:2:2.20	0/0:7:3.70	0/0:3:2.50	./.	0/0:2:2.20	0/0:2:2.20	0/0:1:1.90	./.	0/0:2:2.20	0/1:3:0.25	./.	0/0:2:2.20	0/0:6:3.38	0/0:1:1.89	0/0:6:0.36	./.	./.	0/0:4:2.80	0/0:1:1.90	0/2:5:0.50	0/0:1:1.90	0/0:4:2.80	0/0:2:2.20	0/0:4:2.80
-1	10000809	.	G	A	1.15	.	AF=0.01;NS=60;SB=-0.12	GT:RD:GQ	0/0:1:2.15	0/0:4:2.99	0/0:1:2.15	0/0:3:2.75	./.	0/0:3:2.75	./.	0/0:1:2.14	0/0:3:2.74	0/0:1:2.15	0/0:2:2.45	0/0:1:2.15	./.	0/0:5:3.19	0/0:4:3.05	0/0:6:3.65	0/0:3:2.75	0/0:1:2.15	0/0:5:3.35	0/0:6:3.65	./.	0/0:1:2.15	0/0:1:2.15	0/0:2:2.45	0/0:1:2.15	0/0:3:2.75	0/0:3:2.75	0/0:4:2.75	0/0:2:2.45	0/0:2:2.45	0/0:5:2.74	0/0:1:2.15	./.	./.	./.	0/0:2:2.45	0/0:2:2.45	0/0:7:3.95	0/0:3:2.75	./.	0/0:2:2.45	0/0:2:2.45	0/0:1:2.15	./.	0/0:2:2.45	0/0:3:2.75	./.	0/0:2:2.45	0/0:4:3.04	0/0:1:2.13	0/0:6:3.65	./.	./.	0/0:4:3.05	0/0:1:2.15	1/0:5:0.07	0/0:1:2.15	0/0:4:3.05	0/0:3:2.75	0/0:2:2.45
-1	10000811	.	T	C	0.00	.	AF=0.02;NS=60;SB=0.36	GT:RD:GQ	0/0:1:1.61	0/0:4:2.48	0/0:1:1.61	0/0:3:2.21	./.	0/0:3:2.20	./.	0/0:2:1.91	0/0:3:2.21	0/0:1:1.61	0/0:2:1.85	0/0:1:1.61	./.	1/0:5:0.63	0/0:3:2.21	0/0:6:3.11	0/0:3:2.21	0/0:1:1.61	0/0:5:2.73	0/0:6:2.29	./.	0/0:1:1.61	0/0:2:1.33	0/0:3:1.91	0/0:1:1.61	0/0:3:2.21	0/0:3:2.12	0/0:4:2.31	0/0:2:1.91	0/0:2:1.91	0/0:5:2.61	0/0:1:1.61	./.	./.	./.	0/0:2:1.91	0/0:2:1.91	0/0:7:3.41	0/0:3:2.21	0/0:1:1.31	0/0:2:1.91	0/0:2:1.91	0/0:1:1.61	./.	0/0:2:1.91	0/0:3:2.21	./.	0/0:2:1.88	0/0:4:2.48	0/0:1:1.59	0/0:6:0.47	./.	./.	0/0:4:2.51	0/0:1:1.61	1/0:5:0.33	./.	0/0:4:2.51	0/0:3:2.21	0/0:2:1.87
-1	10000812	.	G	A	0.00	.	AF=0.02;NS=60;SB=0.18	GT:RD:GQ	0/0:1:1.63	0/0:4:2.53	0/0:1:1.63	0/0:3:2.23	./.	0/0:3:2.21	./.	0/0:2:1.92	0/0:3:2.23	0/0:2:1.93	0/0:2:1.82	0/0:2:1.91	./.	1/0:5:0.94	0/0:3:2.23	0/0:6:3.13	0/0:3:2.23	0/0:1:1.63	0/0:5:2.83	0/0:6:3.12	./.	0/0:2:1.93	0/0:2:1.93	0/0:3:2.23	0/0:1:1.63	0/0:3:2.23	0/0:3:2.23	0/0:4:2.23	0/0:2:1.93	0/0:2:1.93	0/0:5:2.50	0/0:1:1.63	./.	./.	./.	0/0:2:1.93	0/0:2:1.93	0/0:7:3.44	0/0:3:2.23	0/0:1:1.63	0/0:2:1.93	0/0:2:1.93	0/0:1:1.63	./.	0/0:2:1.93	0/0:3:2.23	./.	0/0:2:1.63	0/0:4:2.52	0/0:1:1.60	0/0:6:3.13	./.	./.	0/0:4:2.53	0/0:1:1.63	1/0:5:0.69	./.	0/0:4:2.53	0/0:3:2.23	0/0:2:1.93
-1	10000813	.	G	C	2.67	.	AF=0.01;NS=60;SB=-0.28	GT:RD:GQ	0/0:1:2.02	0/0:4:2.92	0/0:2:2.02	0/0:3:2.62	./.	0/0:3:2.62	./.	0/0:2:2.32	0/0:3:2.62	0/0:2:2.32	0/0:3:2.32	1/0:2:0.46	./.	0/0:5:3.22	0/0:3:2.62	0/0:6:3.53	0/0:3:2.62	0/0:1:2.02	0/0:5:3.23	0/0:5:3.23	0/0:1:2.02	0/0:2:2.32	0/0:2:2.32	0/0:3:2.62	0/0:1:2.02	0/0:3:2.62	0/0:3:2.62	0/0:3:2.62	0/0:2:2.32	0/0:3:2.62	0/0:5:3.22	0/0:1:2.02	./.	./.	./.	0/0:2:2.21	0/0:2:2.32	0/0:7:3.83	0/0:3:2.62	0/0:1:2.02	0/0:2:2.32	0/0:2:2.32	0/0:2:2.02	./.	0/0:2:2.32	0/0:3:2.62	./.	0/0:1:2.02	0/0:4:2.92	0/0:1:2.02	0/0:6:3.53	./.	0/0:1:2.02	0/0:4:2.92	0/0:1:2.02	0/0:5:3.23	./.	0/0:4:2.92	0/0:3:2.62	0/0:2:2.32
-1	10000817	.	T	C,G	0.00	.	AF=0.02;NS=60;SB=-0.17	GT:RD:GQ	0/0:2:2.06	0/0:4:2.15	0/0:1:1.76	0/0:2:2.06	./.	0/0:3:1.55	./.	0/0:2:2.06	0/0:2:2.06	0/0:2:2.05	0/0:4:2.60	0/0:2:2.06	./.	0/0:5:2.97	0/0:3:2.37	0/0:6:3.27	0/0:3:2.36	0/0:1:1.76	0/0:4:2.48	0/0:5:2.45	0/0:1:1.76	0/0:2:2.06	0/0:2:0.66	0/0:3:2.37	0/0:1:1.76	0/0:3:2.36	0/0:4:2.61	0/0:3:2.36	0/0:2:2.06	1/0:3:0.10	0/0:5:2.95	0/0:1:1.76	./.	./.	./.	0/0:2:2.06	0/0:2:2.06	0/0:7:3.57	0/0:3:2.37	0/0:2:2.06	0/0:2:2.06	2/0:2:0.76	0/0:3:2.36	./.	0/0:2:2.06	0/0:3:2.37	0/0:1:1.76	0/0:1:1.46	0/0:3:1.93	./.	0/0:6:3.27	./.	0/0:1:1.76	1/0:4:0.48	0/0:1:1.76	0/0:5:2.66	./.	0/0:3:2.37	0/0:3:2.36	0/0:2:1.63
-1	10000823	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.40	GT:RD:GQ	0/0:2:2.22	0/0:5:3.11	0/0:1:1.92	0/0:2:2.21	./.	0/0:3:2.51	./.	0/0:2:2.22	0/0:2:2.22	0/0:2:2.22	0/0:4:2.82	0/0:3:2.52	./.	0/0:5:3.12	0/0:3:2.52	0/0:6:3.42	0/0:3:2.52	./.	0/0:3:2.52	0/0:3:2.45	0/0:1:1.92	0/0:2:2.21	0/0:1:1.89	0/0:2:2.22	0/0:1:1.92	0/0:2:2.19	0/0:4:2.77	0/0:3:2.52	0/0:2:2.22	0/0:3:2.52	0/0:4:2.80	0/0:2:2.22	./.	./.	0/0:1:1.62	0/0:2:2.19	0/0:1:1.92	0/0:7:3.73	0/0:3:2.52	0/0:5:3.12	0/0:1:1.92	0/0:1:1.92	0/0:3:2.22	./.	0/0:3:2.52	1/0:3:1.02	0/0:2:2.21	0/0:2:2.22	0/0:3:2.00	0/0:1:1.62	0/0:6:3.42	./.	0/0:1:1.92	0/0:4:2.82	0/0:1:1.92	0/0:4:2.82	./.	0/0:3:2.52	0/0:3:2.52	0/0:1:1.92
-1	10000824	.	G	C	0.00	.	AF=0.01;NS=60;SB=1.54	GT:RD:GQ	0/0:2:2.20	0/0:4:2.80	0/0:1:1.90	0/0:2:2.20	./.	0/0:3:2.50	./.	0/0:2:2.20	0/0:2:2.20	0/0:2:2.20	0/0:4:2.74	0/0:3:2.50	./.	0/0:5:3.10	0/0:3:2.50	0/0:6:3.40	0/0:3:2.50	./.	0/0:3:2.50	0/0:2:2.16	0/0:1:1.90	0/0:2:2.20	0/0:1:1.90	0/0:2:2.20	0/0:1:1.90	0/0:2:2.20	0/0:3:2.49	0/0:4:2.80	0/0:2:2.20	0/0:3:2.50	0/0:4:2.78	0/0:2:2.20	./.	./.	0/0:1:1.90	0/0:2:2.20	0/0:1:1.90	0/0:7:3.70	0/0:3:2.50	0/0:5:3.10	0/0:1:1.90	0/0:1:1.90	0/0:3:2.47	./.	0/0:3:2.50	1/0:3:1.98	0/0:2:2.20	0/0:2:2.20	0/0:4:2.80	0/0:1:1.90	0/0:6:3.40	./.	0/0:1:1.90	0/0:4:2.80	0/0:1:1.90	0/0:3:2.50	./.	0/0:3:2.50	0/0:3:2.50	0/0:1:1.90
-1	10000828	.	C	T	1.12	.	AF=0.01;NS=60;SB=-0.12	GT:RD:GQ	0/0:4:3.07	0/0:4:3.03	0/0:1:2.16	./.	./.	0/0:2:2.47	./.	0/0:1:2.16	0/0:2:2.46	0/0:2:2.47	0/0:5:3.23	0/0:3:2.77	./.	0/1:6:0.06	0/0:3:2.77	0/0:6:3.67	0/0:3:2.77	./.	0/0:3:2.77	0/0:2:2.46	0/0:1:2.16	0/0:2:2.46	0/0:1:2.16	0/0:1:2.16	0/0:1:2.16	0/0:2:2.33	0/0:2:2.43	0/0:4:2.58	0/0:2:2.46	0/0:3:2.77	0/0:4:2.77	0/0:2:2.47	0/0:1:2.16	./.	0/0:1:2.16	0/0:2:2.44	0/0:1:2.16	0/0:7:3.97	0/0:2:2.47	0/0:5:3.36	0/0:1:2.16	0/0:1:2.16	0/0:3:2.28	./.	0/0:3:2.77	0/0:3:2.77	0/0:2:2.46	0/0:2:2.47	0/0:4:3.07	0/0:1:2.16	0/0:6:3.67	./.	0/0:1:2.16	0/0:5:3.37	./.	0/0:4:3.07	./.	0/0:2:2.46	0/0:4:2.99	0/0:1:1.86
-1	10000829	.	T	G	0.00	.	AF=0.05;NS=60;SB=0.91	GT:RD:GQ	0/0:4:2.18	0/0:4:2.11	0/0:1:1.28	./.	./.	0/0:2:1.50	./.	0/0:2:1.28	0/0:2:1.58	0/0:3:1.89	0/0:5:2.49	0/0:5:2.31	./.	1/0:6:1.25	0/0:3:1.89	0/0:6:2.79	0/0:4:2.16	./.	0/0:3:1.88	0/0:2:1.58	0/0:1:1.28	0/0:2:1.58	0/0:1:1.28	0/0:1:1.28	0/0:1:1.28	0/0:3:1.89	0/0:2:1.58	0/0:4:1.88	0/0:2:1.58	0/0:3:1.89	0/0:3:1.89	0/0:2:1.58	0/0:1:1.28	./.	0/0:2:1.58	0/0:2:1.58	0/0:1:1.28	0/0:7:3.09	0/0:2:1.58	0/0:5:2.47	0/0:1:1.28	0/0:1:1.22	0/0:3:1.01	./.	0/0:3:1.86	0/0:3:1.89	0/0:2:1.58	0/0:2:1.58	0/0:4:2.10	0/0:1:1.28	1/0:6:0.92	./.	0/0:1:1.28	1/0:5:0.92	0/0:1:1.28	1/0:4:1.72	./.	0/0:2:1.58	0/0:4:2.18	./.
-1	10000831	.	G	T	0.00	.	AF=0.01;NS=60;SB=2.55	GT:RD:GQ	0/0:4:2.82	0/0:4:2.83	0/0:2:2.18	./.	./.	0/0:2:2.23	./.	0/0:2:2.23	0/0:2:2.22	0/0:3:2.53	0/0:7:3.67	0/0:5:2.44	./.	0/0:6:3.41	0/0:3:2.53	0/0:6:3.43	0/0:4:1.77	0/0:1:1.93	0/0:3:2.53	0/0:1:1.93	0/0:1:1.93	0/0:2:2.18	0/0:1:1.92	0/0:1:1.93	0/0:1:1.93	0/0:2:2.23	0/0:2:2.08	0/0:3:2.53	0/0:2:2.23	0/0:3:2.53	0/0:4:2.23	0/0:2:2.23	0/0:1:1.93	./.	0/0:2:2.23	0/0:3:2.46	0/0:1:1.93	0/0:7:3.73	0/0:2:2.23	0/0:5:3.13	0/0:1:1.93	0/0:1:0.13	0/0:3:2.53	./.	0/0:3:2.53	0/0:3:2.53	0/0:3:2.04	0/0:2:2.23	0/0:4:2.81	0/0:1:1.93	0/0:6:3.43	./.	0/0:1:1.93	0/0:5:3.13	0/0:1:1.93	0/1:4:0.91	./.	0/0:2:2.22	0/0:4:2.83	./.
-1	10000833	.	T	A	0.00	.	AF=0.02;NS=60;SB=2.54	GT:RD:GQ	0/0:4:1.38	0/0:4:2.67	0/0:2:1.62	./.	./.	0/0:2:2.09	./.	0/0:2:1.87	0/0:2:0.53	0/0:3:2.39	0/0:7:3.45	0/0:5:1.25	./.	0/0:5:2.98	0/0:3:2.39	0/0:6:3.30	0/0:4:1.98	0/0:1:1.79	0/0:2:2.09	0/0:1:1.79	0/0:1:1.79	0/0:1:1.79	1/0:1:1.00	0/0:1:1.79	0/0:1:1.79	0/0:2:2.09	0/0:1:1.79	0/0:3:2.09	0/0:2:2.09	0/0:3:2.39	0/0:4:2.39	0/0:2:2.09	0/0:1:1.79	./.	0/0:2:2.09	0/0:3:1.92	0/0:1:1.79	0/0:7:3.60	0/0:2:2.09	0/0:5:2.95	0/0:2:2.09	0/0:1:1.79	0/0:4:2.54	0/0:1:1.79	0/0:3:2.37	0/0:3:2.39	0/0:3:2.39	0/0:2:2.09	0/0:3:2.39	0/0:1:1.79	0/0:6:3.30	./.	0/0:1:1.79	0/0:5:3.00	0/0:1:1.79	0/0:4:2.70	./.	0/0:2:2.09	0/0:4:2.52	./.
-1	10000834	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.58	GT:RD:GQ	0/0:4:2.86	0/0:4:2.85	0/0:2:2.26	./.	./.	0/0:2:2.26	./.	0/0:2:1.65	0/0:2:2.25	0/0:3:2.55	0/0:8:4.06	0/0:5:3.14	./.	0/1:5:0.76	0/0:3:2.56	0/0:6:3.46	0/0:4:2.81	0/0:1:1.96	0/0:2:2.26	0/0:1:1.94	0/0:1:1.96	0/0:1:1.96	0/0:1:1.95	0/0:1:1.96	0/0:1:1.96	0/0:3:2.46	0/0:1:1.95	0/0:2:2.26	0/0:2:2.23	0/0:3:2.56	0/0:3:2.56	0/0:2:2.26	0/0:1:1.96	./.	0/0:2:2.26	0/0:3:2.54	0/0:1:1.96	0/0:7:3.76	0/0:2:2.26	0/0:6:3.16	0/0:2:2.26	0/0:1:1.96	0/0:4:2.86	0/0:1:1.96	0/0:3:2.56	0/0:3:2.56	0/0:3:2.56	0/0:2:2.26	0/0:3:2.56	0/0:1:1.96	0/0:6:3.46	./.	0/0:1:1.96	0/0:5:3.16	0/0:1:1.96	0/0:4:2.86	./.	0/0:2:2.26	0/0:4:2.86	./.
-1	10000835	.	A	G	0.00	.	AF=0.02;NS=60;SB=0.64	GT:RD:GQ	0/0:4:2.51	0/0:4:2.48	0/0:2:1.91	./.	./.	0/0:2:1.91	./.	0/0:1:1.61	0/0:2:1.89	0/0:3:2.21	0/0:8:3.72	0/0:5:2.71	./.	0/1:5:0.43	0/0:3:2.21	0/0:6:3.12	0/0:4:2.49	0/0:1:1.61	0/0:2:1.91	0/0:1:1.61	0/0:1:1.61	0/0:1:1.61	0/0:1:1.61	0/0:1:1.31	0/0:1:1.61	0/0:3:2.09	0/0:1:1.61	0/0:2:1.91	0/0:2:1.91	0/0:4:2.51	0/0:3:2.21	0/0:2:1.91	0/0:1:1.61	./.	0/0:2:1.91	0/0:3:2.16	0/0:1:1.61	0/0:7:3.42	0/0:2:1.91	0/0:6:2.81	0/0:2:1.91	0/0:1:1.61	0/0:4:2.51	0/0:1:1.61	0/0:3:2.21	0/0:3:2.21	0/0:3:2.21	0/0:2:1.91	0/0:3:2.21	0/0:1:1.61	0/0:6:0.17	./.	0/0:1:1.61	0/0:5:2.82	0/0:1:1.61	0/1:5:0.53	./.	0/0:2:1.91	0/0:4:2.51	./.
-1	10000836	.	C	T	0.00	.	AF=0.01;NS=60;SB=0.03	GT:RD:GQ	0/0:4:2.80	0/0:4:2.83	0/0:2:2.24	./.	./.	0/0:2:2.24	./.	0/0:1:1.94	0/0:2:2.18	0/0:3:2.37	0/0:10:4.34	0/0:5:3.13	./.	0/0:5:0.21	0/0:3:2.53	0/0:6:3.43	0/0:4:2.82	0/0:1:1.94	0/0:2:2.24	0/0:1:1.94	0/0:1:1.94	0/0:1:1.94	0/0:1:1.92	./.	0/0:1:1.94	0/0:2:2.24	0/0:1:1.65	0/0:2:2.24	0/0:2:2.20	0/0:4:2.84	0/0:3:2.53	0/0:2:2.24	0/0:1:1.94	./.	0/0:2:2.24	0/0:3:2.52	0/0:1:1.93	0/0:7:3.71	0/0:2:2.24	0/0:5:3.14	0/0:2:2.24	0/0:1:1.94	0/0:4:2.84	0/0:1:1.93	0/0:3:2.54	0/0:3:2.54	0/0:3:2.40	0/0:3:2.54	0/0:3:2.54	0/0:1:1.94	0/1:6:0.14	./.	0/0:1:1.94	0/0:5:3.14	0/0:1:1.94	0/0:5:3.14	./.	0/0:1:1.93	0/0:4:2.84	./.
-1	10000837	.	G	A	0.00	.	AF=0.03;NS=60;SB=0.34	GT:RD:GQ	0/0:4:2.34	0/0:4:1.21	0/0:2:1.31	./.	./.	0/0:2:1.74	./.	0/0:1:1.44	0/0:1:1.44	0/0:3:2.04	0/0:10:3.61	0/0:5:2.45	./.	1/0:5:1.06	0/0:3:2.04	0/0:6:2.94	0/0:4:1.21	0/0:1:1.44	0/0:1:1.44	0/0:1:1.44	0/0:1:1.44	0/0:1:1.44	0/0:1:1.40	./.	0/0:1:1.44	0/0:2:1.74	0/0:1:1.13	0/0:2:1.74	0/0:2:1.73	1/0:4:0.32	0/0:3:2.04	0/0:2:1.74	0/0:1:1.44	./.	0/0:2:1.74	0/0:3:1.94	0/0:1:1.44	0/0:7:3.24	0/0:2:1.74	0/0:6:2.94	0/0:2:1.74	0/0:1:1.44	0/0:4:1.69	0/0:1:1.44	0/0:3:2.03	0/0:3:2.04	0/0:3:2.02	0/0:3:2.04	0/0:4:2.34	0/0:1:1.44	0/0:6:2.94	./.	0/0:1:1.44	0/0:5:2.64	0/0:1:1.44	1/0:5:0.88	./.	0/0:1:1.44	0/0:4:2.15	./.
-1	10000844	.	C	T	2.57	.	AF=0.01;NS=60;SB=-0.27	GT:RD:GQ	0/0:4:2.94	0/0:6:3.54	0/0:1:2.03	0/0:1:2.03	0/0:1:2.03	0/0:1:1.94	./.	0/0:1:1.72	0/0:3:2.63	0/0:2:2.33	0/0:7:3.84	0/0:5:3.23	./.	0/0:5:3.24	0/0:3:2.64	0/0:6:3.54	0/0:4:2.92	0/0:1:2.03	0/0:1:2.03	0/0:1:2.03	0/0:1:2.03	0/0:1:2.03	0/0:2:2.31	0/0:1:2.03	0/0:1:2.03	0/0:3:2.64	0/0:2:2.33	0/0:2:2.33	0/0:2:2.33	0/0:4:2.91	0/0:3:2.64	0/0:2:2.33	0/0:1:2.03	./.	0/0:2:2.33	0/0:2:2.33	./.	0/0:7:3.84	0/0:2:2.33	0/0:6:3.54	0/0:3:2.64	0/0:2:2.33	0/0:2:2.33	0/0:1:2.03	0/0:3:2.56	0/0:3:2.64	0/0:3:2.63	0/0:2:2.33	0/0:6:3.54	0/0:1:2.03	0/0:6:3.54	./.	0/0:2:2.33	0/0:5:3.24	0/0:1:2.03	0/1:5:0.43	./.	0/0:1:2.03	0/0:4:2.92	./.
-1	10000848	.	C	T	2.51	.	AF=0.01;NS=60;SB=-0.26	GT:RD:GQ	0/0:4:2.95	0/0:6:3.55	0/0:1:2.04	0/0:1:2.04	0/0:1:2.04	0/0:1:2.02	./.	0/0:1:2.04	0/0:3:2.60	0/0:3:2.64	0/0:7:2.75	0/0:5:2.86	./.	0/0:5:3.24	0/0:3:2.65	0/0:6:3.55	0/0:6:3.50	0/0:1:2.04	0/0:1:2.04	0/0:1:2.04	0/0:2:1.96	0/0:1:2.04	0/0:2:2.30	0/0:1:2.04	0/0:2:2.35	0/0:3:2.65	0/0:3:2.35	0/0:1:2.04	0/0:5:2.94	0/0:4:2.95	0/0:4:2.95	0/0:3:2.64	0/0:1:2.04	./.	0/0:1:2.04	0/0:2:2.34	./.	0/0:7:3.84	0/0:2:2.35	0/0:6:3.54	0/0:3:2.65	0/0:2:2.34	0/0:1:2.04	0/0:1:2.04	0/0:3:2.62	0/0:3:2.65	0/0:3:2.61	0/0:2:2.34	0/0:5:3.25	./.	0/0:6:3.55	0/0:3:2.63	0/0:2:2.35	0/0:5:3.25	0/0:1:2.04	0/1:5:0.42	./.	0/0:1:2.04	0/0:4:2.87	./.
-1	10000849	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.32	GT:RD:GQ	0/0:4:2.82	0/0:6:2.81	0/0:1:0.68	0/0:2:2.21	0/0:1:1.91	0/0:1:1.91	./.	0/0:1:1.91	0/0:4:2.78	0/0:3:2.46	0/0:7:2.62	0/0:5:3.12	./.	0/0:5:3.12	0/0:3:2.52	0/0:6:3.42	0/0:5:3.06	0/0:1:1.91	0/0:1:1.91	0/0:1:1.91	0/0:2:2.20	./.	0/0:2:2.21	0/0:2:1.91	0/0:2:2.22	0/0:3:2.52	0/0:3:2.52	0/0:1:1.91	0/0:5:3.11	0/0:3:2.51	0/0:4:2.82	0/0:3:2.51	0/0:1:1.91	./.	0/0:1:1.91	0/0:2:2.21	./.	0/0:7:3.72	0/0:2:2.22	0/0:6:3.40	0/0:3:2.52	0/0:2:2.22	0/0:1:1.89	0/0:1:1.91	0/0:3:2.52	0/1:3:1.31	0/0:3:2.51	0/0:4:2.21	0/0:5:3.12	./.	0/0:6:3.42	0/0:3:2.51	0/0:2:2.20	0/0:5:3.12	0/0:1:1.91	0/0:5:3.12	./.	0/0:1:1.91	0/0:4:2.80	./.
-1	10000850	.	A	G	0.00	.	AF=0.01;NS=60;SB=2.41	GT:RD:GQ	0/0:4:2.85	0/0:6:3.20	0/0:1:1.95	0/0:2:2.25	0/0:1:1.95	0/0:1:1.94	./.	0/0:1:1.95	0/0:4:2.85	0/0:3:2.43	0/0:7:2.87	0/0:5:3.13	./.	0/0:4:2.85	0/0:3:2.55	0/0:6:3.45	0/0:5:3.14	0/0:1:1.95	0/0:1:1.95	0/0:1:1.95	0/0:2:2.23	./.	0/0:2:2.24	0/0:2:2.25	0/0:2:2.25	0/0:3:2.55	0/0:3:2.47	0/0:1:1.95	0/0:5:3.15	0/0:3:2.55	0/0:4:2.85	0/0:3:2.55	0/0:1:1.95	./.	0/0:1:1.95	0/0:2:2.21	./.	0/0:7:3.75	0/0:2:2.25	0/0:6:3.44	0/0:3:2.55	0/0:2:2.25	0/0:1:1.95	0/0:1:1.95	0/0:3:2.55	0/1:3:1.00	0/0:3:2.55	0/0:4:2.85	0/0:5:3.15	./.	0/0:6:3.45	0/0:3:2.55	0/0:1:1.94	0/0:5:3.15	0/0:1:1.95	0/0:5:3.15	./.	0/0:1:1.95	0/0:3:2.55	./.
-1	10000851	.	G	A,T	2.98	.	AF=0.01;NS=60;SB=-3.00	GT:RD:GQ	0/0:4:2.97	0/0:7:3.29	0/0:1:2.07	0/0:2:2.37	0/0:1:2.07	0/0:1:2.07	./.	0/0:1:2.07	0/0:4:2.96	1/0:3:0.09	0/0:7:3.85	0/0:5:3.24	./.	0/0:4:2.97	0/0:3:2.67	0/0:6:3.57	0/0:5:3.27	0/0:1:2.07	0/0:1:2.07	0/0:1:2.06	0/0:2:1.36	./.	0/0:2:2.36	0/0:2:2.37	0/0:2:2.37	0/0:3:2.67	0/0:3:2.63	0/0:2:2.37	0/0:5:3.21	0/0:3:2.67	0/0:4:2.97	0/0:3:2.64	0/0:1:2.07	./.	0/0:1:2.07	0/0:2:2.37	./.	0/0:7:3.86	0/0:2:2.37	0/0:5:3.26	0/0:3:2.67	0/0:2:2.37	0/0:1:2.02	0/0:1:2.07	0/0:3:2.66	0/0:3:2.67	0/0:3:2.18	0/0:4:2.97	0/0:5:3.27	0/0:1:1.77	0/2:6:0.26	0/0:3:2.18	0/0:1:2.07	0/0:5:3.27	0/0:1:2.07	0/0:5:3.27	./.	0/0:1:2.07	0/0:3:1.91	./.
-1	10000856	.	G	T	0.00	.	AF=0.01;NS=60;SB=2.74	GT:RD:GQ	0/0:3:2.60	0/0:6:3.50	0/0:1:2.00	0/0:2:2.30	0/0:1:2.00	0/0:1:1.79	./.	./.	0/0:4:2.90	0/0:3:2.28	0/0:7:3.80	0/0:5:3.18	./.	0/0:4:2.90	0/0:3:2.60	0/0:6:3.50	0/0:5:3.20	./.	0/0:1:2.00	0/0:1:2.00	0/0:2:2.29	./.	0/0:2:1.34	0/0:2:2.30	0/0:2:2.30	0/0:3:2.60	0/0:3:2.50	0/0:2:2.30	0/0:7:3.80	0/0:3:2.60	0/0:5:2.90	0/0:3:2.59	0/0:1:1.99	./.	0/0:1:1.89	0/0:1:2.00	0/0:1:2.00	0/0:6:3.50	0/0:2:2.30	0/0:3:2.54	0/0:3:2.60	0/0:2:2.30	0/0:1:2.00	0/0:1:2.00	0/0:3:2.54	0/0:3:2.60	0/0:3:1.38	0/0:4:2.90	0/0:5:3.20	0/0:1:2.00	0/1:6:0.43	0/0:3:2.31	0/0:1:2.00	0/0:5:3.20	0/0:1:2.00	0/0:5:3.20	./.	0/0:1:2.00	0/0:3:2.60	./.
-1	10000857	.	C	T	0.00	.	AF=0.01;NS=60;SB=2.57	GT:RD:GQ	0/0:3:2.56	0/0:7:3.64	0/0:1:1.96	0/0:2:2.26	0/0:1:1.96	./.	./.	./.	0/0:4:2.86	0/0:3:2.44	0/0:7:3.46	0/0:5:2.99	./.	0/1:4:0.77	0/0:3:2.56	0/0:6:3.46	0/0:5:3.15	./.	0/0:1:1.96	0/0:1:1.93	0/0:2:2.14	./.	0/0:2:1.82	0/0:2:2.26	0/0:2:2.26	0/0:4:2.56	0/0:3:2.56	0/0:3:2.56	0/0:7:3.42	0/0:4:2.85	0/0:4:2.86	0/0:3:2.50	0/0:1:1.96	./.	0/0:2:1.96	0/0:1:1.96	0/0:1:1.96	0/0:6:3.46	0/0:2:2.26	0/0:3:2.23	0/0:3:2.56	0/0:2:2.26	0/0:1:1.96	0/0:1:1.96	0/0:3:2.51	0/0:3:2.56	0/0:3:2.54	0/0:4:2.86	0/0:5:3.16	0/0:1:1.96	0/0:6:3.45	0/0:3:2.17	0/0:1:1.96	0/0:5:3.16	0/0:1:1.96	0/0:5:3.16	./.	0/0:1:1.96	0/0:3:2.37	./.
-1	10000858	.	G	A	0.00	.	AF=0.02;NS=60;SB=2.62	GT:RD:GQ	0/0:3:2.29	0/0:7:3.39	0/0:1:1.69	0/0:2:1.99	0/0:1:1.69	./.	./.	./.	0/0:5:2.89	0/0:3:2.29	0/0:8:3.79	0/0:5:2.89	./.	0/0:4:2.59	0/0:3:2.29	0/0:6:3.19	0/0:6:2.89	./.	0/0:1:1.69	0/0:1:1.69	0/0:2:1.96	./.	0/0:2:1.95	0/0:2:1.99	0/0:2:1.99	0/0:4:2.59	0/0:3:2.29	0/0:3:2.29	0/0:7:2.83	0/0:4:2.59	0/0:4:2.59	0/0:3:2.29	0/0:1:1.69	./.	0/0:2:1.99	0/0:1:1.69	0/0:1:1.69	0/0:6:3.20	0/0:2:1.99	0/0:3:1.97	0/0:3:2.29	0/0:2:1.99	0/0:1:1.69	0/0:1:1.69	0/0:3:2.29	0/0:3:2.29	0/0:3:2.29	0/0:4:2.59	0/0:5:2.89	0/0:1:1.69	1/0:6:0.53	0/0:4:1.43	0/0:1:1.69	0/0:5:2.89	0/0:1:1.69	1/0:5:0.63	./.	0/0:1:1.69	0/0:3:2.28	./.
-1	10000860	.	C	G	0.00	.	AF=0.01;NS=60;SB=2.46	GT:RD:GQ	0/0:3:2.55	0/0:8:4.05	0/0:1:1.95	0/0:2:2.25	0/0:1:1.94	./.	./.	./.	0/0:5:3.04	0/0:3:2.54	0/0:9:4.05	0/0:4:2.85	./.	0/1:4:0.93	0/0:3:2.55	0/0:6:3.45	0/0:6:3.45	0/0:1:1.65	0/0:1:1.95	0/0:1:1.95	0/0:2:2.25	0/0:1:1.70	0/0:3:2.54	0/0:2:2.25	0/0:2:2.25	0/0:4:2.85	0/0:4:2.47	0/0:3:2.55	0/0:8:3.45	0/0:4:2.85	0/0:4:2.85	0/0:3:2.55	0/0:2:2.25	./.	0/0:2:2.25	0/0:1:1.95	0/0:1:1.95	0/0:7:3.75	0/0:2:2.25	0/0:1:1.95	0/0:3:2.55	0/0:2:2.25	0/0:1:1.95	0/0:1:1.95	0/0:3:2.55	0/0:3:2.55	0/0:3:2.55	0/0:4:2.77	0/0:6:3.45	0/0:1:1.95	0/0:6:3.45	0/0:4:2.84	0/0:1:1.12	0/0:5:3.15	0/0:1:1.95	0/0:5:3.15	./.	0/0:1:1.95	0/0:2:2.25	./.
-1	10000862	.	C	G	39.65	.	AF=0.07;NS=60;SB=-2.32	GT:RD:GQ	0/0:4:2.05	0/0:8:3.26	0/0:1:1.15	0/0:2:1.45	0/0:1:1.13	./.	0/0:1:1.15	./.	0/0:5:2.35	0/0:4:2.02	0/0:8:3.26	0/0:4:2.05	./.	0/1:4:1.93	0/0:4:2.05	0/0:6:2.65	0/0:7:2.95	0/0:1:1.15	0/0:1:1.15	0/0:1:1.14	0/0:3:1.40	0/0:1:1.15	0/0:4:1.85	0/0:2:1.45	0/0:2:1.45	0/0:4:2.05	0/0:4:1.75	0/0:2:1.45	0/0:8:3.26	0/0:4:2.05	0/0:5:2.05	0/0:3:1.74	0/0:2:1.44	./.	0/0:3:1.75	0/0:1:1.15	0/0:1:1.15	0/0:7:2.96	0/0:2:1.45	0/0:1:1.15	0/0:3:1.75	0/0:2:1.45	0/0:1:1.15	0/0:1:1.15	0/0:4:2.05	0/1:3:2.73	0/1:3:0.50	0/0:4:2.05	0/0:6:2.65	0/0:2:1.45	0/1:6:1.42	0/0:4:2.05	0/0:2:1.21	0/1:5:1.92	0/0:1:1.15	0/1:5:1.72	./.	0/0:3:1.75	0/0:2:1.45	./.
-1	10000865	.	C	T	0.00	.	AF=0.05;NS=60;SB=-0.78	GT:RD:GQ	0/0:3:1.90	0/0:7:3.03	0/0:1:1.31	0/0:2:1.61	0/0:1:1.01	./.	0/0:1:1.31	0/0:1:1.01	0/0:4:2.21	0/0:4:2.21	0/0:7:3.12	0/0:3:1.88	./.	0/1:4:1.31	0/0:4:2.21	0/0:6:2.81	0/0:7:2.96	0/0:1:1.31	0/0:1:1.31	0/0:1:1.29	0/0:2:1.31	0/0:1:1.29	0/0:3:1.91	0/0:2:1.31	0/0:2:1.61	0/0:3:1.90	0/0:3:1.91	0/0:2:1.61	0/0:7:3.12	0/0:4:2.21	0/0:4:2.21	0/0:4:2.14	0/0:1:1.31	./.	0/0:3:1.91	0/0:1:1.31	0/0:1:1.31	0/0:7:3.10	0/0:2:1.61	0/0:1:1.31	0/0:3:1.91	0/0:2:1.61	0/0:2:1.31	0/0:1:1.31	0/0:5:2.45	0/1:3:1.81	0/0:3:1.90	0/0:4:1.72	0/0:6:2.80	0/0:2:1.61	0/1:6:0.86	0/0:4:2.19	0/0:2:1.12	0/0:5:2.51	./.	0/1:5:1.06	./.	0/0:3:1.90	0/0:1:1.31	./.
-1	10000872	.	C	T,G	0.00	.	AF=0.01;NS=60;SB=0.30	GT:RD:GQ	0/0:3:2.53	0/0:7:3.75	0/0:1:1.96	0/0:2:2.26	./.	./.	0/0:2:2.26	0/0:2:2.26	0/0:5:0.49	0/0:5:2.30	0/0:3:2.56	0/0:2:2.26	./.	0/1:4:0.96	0/0:4:2.86	0/0:6:3.46	0/0:5:3.14	0/0:2:2.22	0/0:2:2.26	0/0:1:1.96	0/0:2:1.72	0/0:2:2.26	0/0:4:2.54	0/0:1:1.96	0/0:2:2.26	0/0:2:2.20	0/0:3:2.25	0/0:3:2.56	0/0:5:3.16	0/0:4:2.86	0/0:5:3.15	0/0:6:3.41	0/0:1:1.96	0/0:1:1.77	0/0:3:2.56	0/0:1:1.96	0/0:1:1.96	0/0:7:3.76	0/0:2:2.26	0/2:2:0.31	0/0:2:2.26	0/0:1:1.96	0/0:2:2.26	0/0:1:1.96	0/0:5:3.15	0/0:3:2.56	0/0:3:2.17	0/0:4:2.80	0/0:7:3.70	0/0:2:2.26	0/0:6:3.46	0/0:2:2.25	0/0:1:1.96	0/0:4:2.86	0/0:1:1.75	0/0:5:3.16	./.	0/0:3:2.07	0/0:1:1.96	./.
-1	10000874	.	G	A,T	0.00	.	AF=0.04;NS=60;SB=-0.42	GT:RD:GQ	0/0:3:1.94	0/0:8:3.42	0/0:1:1.34	0/0:1:1.34	0/0:1:1.04	./.	0/0:2:1.64	0/0:2:1.65	0/0:5:2.54	0/0:6:2.84	0/0:3:1.94	0/0:2:1.64	./.	1/0:4:1.33	0/0:4:2.24	0/0:6:2.85	0/0:6:2.17	0/0:2:1.64	0/0:2:1.64	0/0:2:1.49	0/0:3:1.93	0/0:3:1.94	0/0:4:2.14	./.	0/0:2:1.64	0/0:2:1.36	0/0:2:1.64	0/0:3:1.94	0/0:5:2.55	0/0:4:2.23	0/0:5:2.53	0/0:5:2.54	0/0:1:1.34	0/0:1:1.33	0/0:3:1.94	0/0:1:1.34	0/0:1:1.34	0/0:7:3.15	0/0:2:1.64	0/0:1:1.34	0/0:2:1.64	0/0:1:1.34	0/0:2:1.63	0/0:1:1.34	0/0:4:2.25	1/0:3:1.83	0/0:3:1.38	0/0:2:1.64	0/0:7:3.15	0/2:2:0.58	1/0:6:0.58	0/0:2:0.71	0/0:1:1.32	0/0:4:2.24	0/0:2:1.64	1/0:5:0.98	./.	0/0:3:1.94	0/0:1:1.34	0/0:1:1.34
-1	10000877	.	T	A,C	0.00	.	AF=0.03;NS=60;SB=1.32	GT:RD:GQ	0/0:3:2.14	0/0:7:3.35	0/0:1:1.54	0/0:1:1.54	0/0:1:1.54	0/0:2:1.84	0/0:2:1.84	0/0:2:1.84	0/0:5:2.75	0/0:6:3.03	0/0:3:2.14	0/0:2:1.84	./.	1/0:3:0.77	0/0:4:2.44	0/0:6:3.05	0/0:6:2.86	0/0:3:1.72	0/0:4:2.45	0/0:2:1.84	0/0:3:2.14	0/0:3:2.14	0/0:4:2.20	./.	0/0:2:1.84	0/0:2:1.83	0/0:3:2.14	0/0:3:2.14	0/0:4:2.22	0/0:4:2.44	0/0:5:2.44	0/0:6:3.00	0/0:1:1.54	0/0:1:1.54	0/0:3:2.14	0/0:2:1.84	./.	0/0:7:3.35	0/0:2:1.84	0/0:1:1.54	0/0:2:1.84	0/0:1:1.54	0/0:3:2.14	0/0:1:1.54	0/0:4:2.44	2/0:3:0.90	2/0:4:1.46	0/0:3:1.84	0/0:6:3.05	0/0:2:1.54	2/0:6:0.10	0/0:2:1.83	0/0:1:1.54	0/0:4:2.44	0/0:3:1.84	0/0:5:2.75	./.	0/0:3:2.04	0/0:1:1.54	0/0:1:1.12
-1	10000878	.	C	A	0.00	.	AF=0.03;NS=60;SB=0.59	GT:RD:GQ	0/0:3:2.18	0/0:6:3.07	0/0:1:1.58	0/0:2:1.88	0/0:1:1.58	0/0:2:1.88	0/0:2:1.88	0/0:3:1.88	0/0:5:2.78	0/0:6:2.19	0/0:3:2.17	0/0:2:1.88	./.	0/0:3:1.85	0/0:4:2.48	0/0:5:0.46	0/0:7:2.39	0/0:3:1.84	0/0:4:2.47	0/0:2:1.87	0/0:3:2.17	0/0:3:2.18	0/0:4:2.27	./.	0/0:2:1.88	0/0:2:1.79	0/0:3:2.17	0/0:3:2.18	0/0:4:1.89	0/0:4:2.48	0/0:4:0.49	0/0:6:2.01	0/0:1:1.58	0/0:1:1.13	0/0:3:2.18	0/0:2:1.88	./.	0/0:7:3.38	0/0:3:2.18	0/0:1:1.58	0/0:1:1.56	0/0:1:1.58	0/0:3:2.18	0/0:1:1.58	0/0:4:2.48	0/0:3:2.18	0/0:4:0.09	0/0:3:2.18	0/0:6:3.08	0/0:2:1.87	0/0:6:0.76	0/0:2:0.75	0/0:1:1.58	1/0:4:3.79	0/0:3:2.18	0/0:5:2.48	./.	0/0:3:2.17	0/0:1:1.58	0/0:1:1.30
-1	10000879	.	A	C	0.00	.	AF=0.02;NS=60;SB=0.57	GT:RD:GQ	0/0:3:2.40	0/0:7:3.61	0/0:1:1.80	0/0:2:2.10	0/0:1:1.80	0/0:2:2.10	0/0:2:2.10	0/0:3:2.16	0/0:5:2.97	0/0:6:3.30	0/0:4:2.58	0/0:2:2.10	./.	0/0:3:2.40	0/0:4:2.70	0/0:5:3.00	0/0:7:3.14	0/0:3:2.04	0/0:4:2.70	0/0:4:2.62	0/0:3:2.28	0/0:3:2.40	0/0:4:2.68	./.	0/0:2:2.10	0/0:2:1.77	0/0:3:2.16	0/0:3:2.40	0/0:4:2.52	0/0:4:2.70	0/0:4:2.46	0/0:6:3.30	0/0:1:1.80	0/0:1:1.80	0/0:3:2.35	0/0:2:2.10	./.	0/0:8:3.91	0/0:3:2.40	0/0:1:1.80	0/0:1:1.80	./.	0/0:3:2.40	0/0:1:1.80	0/0:4:2.70	0/0:3:2.40	0/0:4:2.66	0/0:3:2.40	0/0:6:3.30	0/0:2:2.10	0/0:6:0.25	0/0:2:2.10	0/0:1:1.79	0/1:4:3.30	0/0:4:2.68	0/0:5:3.01	./.	0/0:2:2.10	0/0:1:1.80	0/0:1:1.51
-1	10000880	.	A	C	1.18	.	AF=0.01;NS=60;SB=-0.13	GT:RD:GQ	0/0:3:2.83	0/0:7:4.03	0/0:1:2.22	0/0:2:2.52	0/0:1:2.22	0/0:2:2.52	0/0:2:2.52	0/0:3:1.84	0/0:5:3.39	0/0:5:3.42	0/0:4:3.00	./.	./.	0/0:3:2.83	0/0:4:3.13	0/0:5:3.43	0/0:6:3.27	0/0:3:2.71	0/0:4:3.13	0/0:5:3.42	0/0:3:2.70	0/0:3:2.82	0/0:4:3.12	./.	0/0:2:2.52	0/0:3:2.20	0/0:3:2.58	0/0:3:2.83	0/0:4:2.91	0/0:4:3.13	0/0:4:2.88	0/0:6:3.73	0/0:1:2.22	0/0:1:2.22	0/0:3:2.78	0/0:2:2.52	./.	0/0:8:4.33	0/0:4:3.12	0/0:3:2.22	0/0:1:2.22	./.	0/0:3:2.83	0/0:2:2.52	0/0:4:3.13	0/0:3:2.83	0/0:4:3.11	0/0:3:2.82	0/0:6:3.71	0/0:3:2.52	0/0:6:3.73	0/0:3:2.83	0/0:2:2.52	0/0:4:3.13	0/0:4:3.09	0/1:5:0.08	./.	0/0:2:2.52	0/0:1:2.22	0/0:1:2.22
-1	10000887	.	A	T	0.00	.	AF=0.01;NS=60;SB=2.57	GT:RD:GQ	0/0:4:2.72	0/0:8:3.94	0/0:1:1.84	0/0:2:2.14	0/0:1:1.84	0/0:3:2.44	0/0:3:2.21	0/0:4:2.34	0/0:5:3.04	0/0:5:3.04	0/0:4:2.74	0/0:1:1.84	0/0:1:1.84	0/1:4:0.12	0/0:4:2.74	0/0:4:2.74	0/0:8:3.92	0/0:4:2.74	0/0:6:2.87	0/0:7:3.64	0/0:4:2.74	0/0:3:2.43	0/0:5:2.97	0/0:3:2.34	0/0:2:2.14	0/0:5:2.51	0/0:3:2.14	0/0:4:2.26	0/0:3:2.44	0/0:4:2.74	0/0:2:2.14	0/0:6:3.34	0/0:2:2.14	0/0:2:2.14	0/0:4:2.44	0/0:1:1.84	0/0:2:2.14	0/0:8:3.94	0/0:5:3.04	0/0:4:2.74	0/0:2:2.14	0/0:2:2.14	0/0:2:2.14	0/1:3:0.86	0/0:5:3.04	0/0:3:2.44	0/0:5:3.04	0/0:4:2.74	0/0:6:3.34	0/0:7:3.64	0/0:5:3.04	0/0:4:2.44	0/0:5:3.04	0/0:4:2.74	0/0:5:2.94	0/0:5:3.04	0/0:1:1.84	./.	0/0:1:1.84	0/0:2:2.02
-1	10000888	.	A	C	3.94	.	AF=0.01;NS=60;SB=-0.40	GT:RD:GQ	0/0:4:3.00	0/0:8:4.19	0/0:1:2.09	0/0:2:2.39	0/0:1:2.09	0/0:4:2.99	0/0:3:2.69	0/0:4:2.99	0/0:5:3.28	0/0:6:3.59	0/0:4:3.00	0/0:1:2.08	0/0:1:2.09	0/0:4:2.99	0/0:4:3.00	0/0:4:3.00	0/0:9:4.50	0/0:5:2.99	0/0:6:3.53	0/0:8:4.18	0/0:4:2.99	0/0:3:2.68	0/0:5:3.08	0/0:3:2.68	0/0:2:2.39	0/0:6:3.14	0/0:3:2.66	0/0:3:2.68	0/0:3:2.69	0/0:5:3.30	0/0:3:2.39	0/0:6:3.60	0/0:3:2.69	0/0:2:2.39	0/0:4:2.99	0/0:1:1.97	0/0:2:2.39	0/0:8:4.19	0/0:5:2.65	0/0:4:3.00	0/0:2:2.39	0/0:2:2.39	0/0:2:2.39	0/0:3:2.61	0/0:5:3.30	0/0:3:2.69	0/0:6:3.59	0/0:5:2.92	0/0:5:3.30	0/0:7:3.90	0/0:5:3.30	0/0:4:3.00	0/0:5:3.30	0/0:4:3.00	0/0:5:3.29	0/1:5:0.66	0/0:2:2.39	./.	0/0:1:2.09	0/0:2:2.39
-1	10000890	.	T	A	20.18	.	AF=0.07;NS=60;SB=-2.32	GT:RD:GQ	0/0:4:2.05	0/0:8:3.01	0/0:2:1.15	0/0:2:1.46	0/0:1:1.15	0/0:4:2.03	0/0:4:1.76	0/0:4:1.76	0/0:7:0.75	0/0:6:1.89	0/0:6:2.66	0/0:1:1.15	0/0:1:1.15	0/0:4:2.06	1/0:4:1.11	1/0:3:1.40	0/0:8:3.25	0/0:5:2.36	1/0:6:0.64	0/0:8:3.25	0/0:4:1.33	1/0:3:0.67	0/0:5:2.05	0/0:3:1.75	1/0:2:1.91	0/0:6:2.66	0/0:2:1.45	0/0:3:1.74	0/0:3:1.31	0/0:5:2.35	0/0:4:2.06	0/0:6:1.09	0/0:3:1.72	0/0:2:1.46	0/0:4:1.59	0/0:2:0.90	0/0:2:1.46	0/0:8:3.08	0/0:5:0.30	0/0:4:2.06	0/0:2:1.46	0/0:2:1.46	0/0:1:1.15	0/0:3:1.75	0/0:5:2.36	0/0:2:1.45	0/0:6:2.39	0/0:5:2.35	0/0:4:2.03	0/0:7:2.88	1/0:5:0.80	0/0:5:2.36	0/0:5:2.36	0/0:3:1.75	0/0:5:0.37	0/0:5:2.06	0/0:2:1.45	./.	0/0:1:1.15	0/0:2:1.45
-1	10000897	.	T	A	2.52	.	AF=0.01;NS=60;SB=-0.26	GT:RD:GQ	0/0:6:3.65	0/0:9:4.54	0/0:2:2.31	0/0:3:1.87	0/0:2:2.15	0/0:4:2.64	0/0:5:3.21	0/0:3:2.75	0/0:7:3.92	0/0:7:3.75	0/0:6:3.26	0/0:1:2.15	0/0:1:2.13	0/0:4:3.05	0/0:4:3.05	0/0:3:2.75	0/0:11:3.95	0/0:4:2.82	0/0:6:3.65	0/0:9:4.55	0/0:4:2.80	0/0:3:2.41	0/0:4:2.83	0/0:4:2.99	0/0:2:2.45	0/0:7:3.88	1/0:3:0.41	0/0:5:0.94	0/0:2:2.45	0/0:6:3.65	0/0:5:3.04	0/0:6:3.15	0/0:2:2.45	0/0:2:2.45	0/0:6:3.00	0/0:2:2.04	0/0:2:2.45	0/0:9:4.49	0/0:5:3.34	0/0:4:3.05	0/0:2:2.44	0/0:2:2.45	0/0:2:2.44	0/0:4:2.48	0/0:5:3.35	0/0:3:2.75	0/0:6:3.40	0/0:7:3.95	0/0:3:2.75	0/0:10:4.74	0/0:4:3.05	0/0:7:3.73	0/0:7:3.95	0/0:3:2.75	0/0:5:3.05	0/0:5:3.35	0/0:3:2.61	./.	0/0:1:2.14	0/0:4:2.74
-1	10000900	.	G	A	0.00	.	AF=0.02;NS=60;SB=2.49	GT:RD:GQ	0/0:5:2.93	0/0:9:1.47	0/0:3:2.31	1/0:2:0.72	0/0:1:1.73	0/0:4:2.63	0/0:4:2.63	0/0:3:2.33	0/0:6:3.23	0/0:6:3.20	0/0:7:3.25	0/0:2:2.03	0/0:1:1.73	0/0:3:2.33	0/0:3:2.33	0/0:3:2.33	0/0:9:4.13	0/0:3:2.02	0/0:6:2.85	0/0:9:3.10	0/0:4:2.62	0/0:2:0.64	0/0:4:2.39	0/0:4:2.31	0/0:2:2.03	0/0:7:3.53	0/0:5:2.03	0/0:6:3.17	0/0:1:1.73	0/0:6:3.22	0/0:5:2.92	0/0:6:3.21	0/0:2:2.03	0/0:2:2.03	0/0:5:2.93	0/0:1:1.73	0/0:2:2.03	0/0:9:4.13	1/0:5:0.67	0/0:4:2.63	0/0:4:2.63	0/0:2:2.03	0/0:2:2.03	0/0:6:1.75	0/0:7:3.53	0/0:3:2.33	0/0:6:3.22	0/0:7:3.53	0/0:2:2.03	0/0:9:4.13	0/0:4:2.63	0/0:7:3.47	0/0:6:3.23	0/0:3:2.33	0/0:5:2.93	0/0:4:2.63	0/0:3:2.33	0/0:1:1.43	0/0:1:1.73	0/0:3:2.33
-1	10000901	.	A	G	4.04	.	AF=0.01;NS=60;SB=-0.41	GT:RD:GQ	0/0:4:3.00	0/0:9:4.50	0/0:3:2.70	0/0:2:2.40	0/0:1:2.10	0/0:4:3.00	0/0:4:3.00	0/0:3:2.70	0/0:7:3.91	0/0:6:3.59	0/0:7:3.84	0/0:2:2.38	0/0:1:2.10	0/0:3:2.70	0/0:3:2.70	0/0:3:2.70	0/0:11:4.50	0/0:3:2.69	0/0:6:3.59	0/0:9:4.27	0/0:4:3.00	0/0:2:2.40	0/0:4:2.57	0/0:4:3.00	0/0:2:2.40	0/0:7:3.91	0/0:5:3.28	0/0:7:3.37	0/0:1:2.10	0/0:6:3.60	0/0:5:3.27	0/0:6:3.61	0/0:2:2.40	0/0:2:2.40	0/0:4:3.00	0/0:1:2.10	0/0:2:2.40	0/0:9:4.50	0/1:5:0.68	0/0:4:3.00	0/0:4:3.00	0/0:2:2.40	0/0:2:2.40	0/0:6:3.58	0/0:7:3.91	0/0:3:2.70	0/0:6:3.60	0/0:8:3.91	0/0:2:2.40	0/0:9:4.21	0/0:4:3.00	0/0:7:3.78	0/0:6:3.61	0/0:3:2.70	0/0:7:3.30	0/0:4:3.00	0/0:3:2.70	0/0:1:2.10	0/0:1:2.10	0/0:5:2.69
-1	10000906	.	G	A	1.16	.	AF=0.01;NS=60;SB=-0.12	GT:RD:GQ	0/0:5:2.00	0/0:9:4.28	0/0:8:4.02	0/0:3:2.81	0/0:1:2.26	0/0:5:3.13	0/0:3:2.56	0/0:2:2.56	0/0:8:4.34	0/0:6:3.71	0/0:8:4.06	0/0:2:2.55	0/0:1:2.26	0/0:3:2.86	0/0:3:2.86	0/0:2:2.56	0/0:12:4.95	0/0:5:3.45	0/0:6:3.74	0/0:9:4.65	0/0:4:3.15	0/0:1:2.26	0/0:4:3.13	0/0:5:3.16	0/0:2:2.56	0/0:7:3.76	0/0:5:1.23	0/0:8:3.96	0/0:2:2.26	0/0:7:4.06	0/0:4:3.13	0/0:9:4.31	0/0:3:2.52	0/0:2:2.56	0/0:5:3.32	0/0:1:2.26	0/0:2:2.56	0/0:9:4.64	1/0:5:0.06	0/0:2:2.56	0/0:3:2.86	0/0:2:2.56	0/0:4:2.32	0/0:7:3.92	0/0:7:4.06	0/0:3:2.86	0/0:6:3.75	0/0:7:4.06	0/0:2:2.56	0/0:7:4.04	0/0:4:3.16	0/0:8:3.20	0/0:7:3.76	0/0:3:2.86	0/0:7:4.02	0/0:4:3.16	0/0:3:2.86	0/0:1:2.26	0/0:1:2.25	0/0:6:3.73
-1	10000915	.	G	C	1.71	.	AF=0.01;NS=60;SB=-2.10	GT:RD:GQ	0/0:5:3.44	0/0:11:5.01	0/0:6:3.73	0/0:4:3.02	0/0:5:3.44	0/0:6:3.74	0/0:2:2.51	./.	0/0:8:4.33	0/0:5:3.44	0/0:9:4.64	0/0:4:3.13	0/0:1:2.23	0/0:3:2.83	0/0:3:2.83	0/0:1:2.23	0/0:10:4.94	0/0:4:2.83	0/0:6:3.69	0/0:8:4.32	0/0:5:3.44	0/0:2:2.14	0/0:8:4.04	0/0:3:2.83	0/0:3:2.83	0/0:8:4.03	0/0:6:2.67	0/0:8:4.04	0/0:8:4.34	0/0:7:4.04	0/0:4:3.13	0/0:10:3.06	0/0:3:2.83	0/0:1:2.23	0/0:4:3.13	0/0:2:2.53	0/0:1:2.23	0/0:8:3.61	0/0:5:3.13	0/0:3:1.49	0/0:3:2.83	0/0:4:3.13	0/0:5:2.01	1/0:8:0.24	0/0:6:3.73	0/0:3:2.83	0/0:6:3.73	0/0:6:3.35	0/0:1:2.23	0/0:7:4.04	0/0:5:3.44	0/0:5:3.23	0/0:6:3.74	0/0:3:2.83	0/0:6:3.74	0/0:4:3.13	0/0:2:2.53	0/0:1:2.23	0/0:2:2.53	0/0:6:3.74
-1	10000935	.	C	A	5.17	.	AF=0.01;NS=60;SB=-0.52	GT:RD:GQ	0/0:4:2.95	0/0:8:4.13	0/0:7:3.86	0/0:5:3.26	0/0:6:2.36	0/0:6:3.52	0/0:3:2.66	0/0:3:2.66	0/0:5:3.21	0/0:3:2.66	0/0:15:5.96	0/0:4:2.96	0/0:2:2.35	0/0:3:2.66	0/0:4:2.96	0/0:1:2.05	0/0:11:4.46	0/0:6:3.26	0/0:3:2.66	0/0:5:3.26	0/0:4:2.66	0/0:2:2.36	0/0:5:3.26	0/0:3:2.66	0/0:3:2.66	0/0:9:4.32	0/0:8:4.11	0/0:6:3.56	0/0:12:4.75	0/0:4:2.96	0/0:18:6.85	0/0:8:4.16	0/0:2:2.36	./.	0/0:2:2.35	0/0:5:3.25	./.	0/0:8:4.16	0/0:6:3.56	0/0:5:3.26	0/0:5:3.26	0/0:4:2.96	0/0:8:4.16	0/0:5:3.25	0/0:6:3.56	0/0:1:2.05	0/0:5:1.63	0/0:8:4.16	0/0:1:2.05	0/0:3:2.63	0/0:5:3.26	1/0:4:0.84	0/0:3:2.66	0/0:3:2.66	0/0:5:3.25	0/0:6:3.56	0/0:1:2.05	./.	0/0:4:2.96	0/0:1:2.05
-1	10000964	.	T	C	0.00	.	AF=0.01;NS=60;SB=2.23	GT:RD:GQ	0/0:3:2.61	0/0:7:3.84	0/0:3:2.33	0/0:3:2.63	0/0:3:2.63	0/0:10:4.71	0/0:1:2.03	0/0:3:2.63	1/0:3:1.16	0/0:5:3.23	0/0:14:5.94	./.	0/0:2:2.31	0/0:3:2.63	0/0:4:2.93	0/0:1:2.03	0/0:8:4.13	0/0:2:2.33	0/0:4:2.93	0/0:5:3.23	0/0:4:2.93	0/0:3:2.63	0/0:3:2.63	0/0:3:2.63	0/0:3:2.63	0/0:4:2.93	0/0:4:2.92	0/0:8:4.14	0/0:9:4.43	0/0:5:3.23	0/0:7:3.84	0/0:2:2.33	0/0:3:2.63	0/0:1:2.03	0/0:4:2.93	0/0:1:2.03	0/0:2:2.25	0/0:7:3.83	0/0:6:3.53	0/0:5:3.23	0/0:7:3.83	0/0:4:2.93	0/0:6:3.53	0/0:3:2.63	0/0:5:3.23	0/0:2:2.33	0/0:2:2.33	0/0:6:3.41	0/0:4:2.93	0/0:3:2.63	0/0:6:3.53	0/0:6:3.53	0/0:3:2.63	0/0:3:2.63	0/0:2:2.33	0/0:7:3.83	0/0:1:1.97	0/0:2:2.33	0/0:3:2.62	./.
-1	10000978	.	G	A	3.17	.	AF=0.01;NS=60;SB=-0.33	GT:RD:GQ	0/0:4:2.86	0/0:7:3.87	0/0:2:2.39	0/0:3:2.63	0/0:2:2.09	0/0:8:4.19	0/0:3:2.69	0/0:1:1.79	0/0:5:3.29	0/0:5:3.29	0/0:15:5.98	0/0:4:2.99	0/0:1:2.09	0/0:2:2.38	0/0:4:2.99	0/0:1:2.09	0/0:5:2.99	0/0:1:2.09	0/0:3:2.69	0/0:4:2.99	0/0:3:2.65	0/0:2:2.38	0/0:2:2.39	0/0:1:2.09	0/0:2:2.39	0/0:4:2.69	1/0:4:0.54	0/0:5:3.29	0/0:4:2.64	0/0:5:3.29	0/0:6:3.59	0/0:3:2.69	0/0:3:2.69	0/0:1:2.09	0/0:9:4.19	0/0:1:2.09	0/0:2:2.32	0/0:7:3.89	0/0:6:3.59	0/0:3:2.69	0/0:7:3.89	0/0:3:2.69	0/0:7:3.85	0/0:2:2.39	0/0:4:2.99	0/0:1:2.09	0/0:1:2.09	0/0:2:2.34	0/0:6:3.57	0/0:5:3.27	0/0:5:3.29	0/0:4:2.99	0/0:8:3.81	0/0:2:2.39	0/0:4:2.92	0/0:7:3.88	./.	./.	0/0:3:2.69	0/0:1:2.09
-1	10000995	.	T	A,C	5.02	.	AF=0.01;NS=60;SB=-2.85	GT:RD:GQ	0/0:5:3.31	1/0:4:0.43	0/0:4:2.64	0/0:5:3.31	0/0:2:2.18	0/0:4:3.01	0/0:3:2.60	./.	0/0:4:3.01	0/0:4:3.00	0/0:13:5.71	0/0:4:3.01	0/0:2:2.41	0/0:2:2.41	0/0:4:3.01	0/0:2:2.41	0/0:7:3.89	0/0:4:2.71	0/0:4:2.61	0/0:5:3.30	0/0:5:3.31	0/0:1:2.11	0/0:4:2.98	./.	0/0:3:2.71	0/0:8:4.22	0/0:3:2.67	0/0:4:3.01	0/0:5:3.08	0/0:6:3.61	0/0:7:3.91	0/0:4:3.01	0/0:1:2.11	0/0:1:2.11	0/0:9:4.52	./.	0/0:1:2.11	0/0:8:4.22	0/0:6:3.61	0/0:2:2.41	0/0:8:4.22	0/0:3:2.71	0/0:5:3.28	0/0:1:2.11	0/0:6:3.60	0/0:2:2.41	0/0:1:2.11	0/0:2:2.41	0/0:6:3.60	0/0:3:2.70	0/0:5:3.31	./.	0/0:8:4.16	2/0:2:0.43	0/0:6:3.61	0/0:7:3.91	0/0:1:2.11	0/0:1:1.81	0/0:3:2.71	0/0:5:3.31
-1	10000996	.	G	T	1.71	.	AF=0.01;NS=60;SB=-0.18	GT:RD:GQ	0/0:5:3.40	0/0:4:3.09	0/0:4:3.09	0/0:5:3.40	0/0:2:2.22	0/0:4:3.10	0/0:4:2.80	./.	0/0:4:3.10	0/0:4:3.08	0/0:13:5.80	0/0:4:3.10	0/0:2:2.50	0/0:2:2.50	0/0:4:3.10	0/0:2:2.50	0/0:7:3.45	0/0:3:2.78	0/1:4:0.24	0/0:5:3.40	0/0:5:3.37	0/0:1:2.20	0/0:4:3.08	./.	0/0:3:2.80	0/0:8:4.31	0/0:3:2.73	0/0:5:3.40	0/0:5:3.12	0/0:6:3.70	0/0:7:4.00	0/0:4:3.10	0/0:1:2.20	0/0:1:2.20	0/0:9:4.46	0/0:1:2.20	0/0:1:2.20	0/0:8:4.31	0/0:6:3.70	0/0:2:2.50	0/0:7:4.00	0/0:2:2.50	0/0:5:2.80	0/0:1:2.19	0/0:6:3.68	0/0:2:2.50	0/0:1:2.20	0/0:2:2.50	0/0:6:3.70	0/0:3:2.79	0/0:5:3.40	./.	0/0:7:3.99	0/0:2:2.50	0/0:6:3.70	0/0:7:4.00	0/0:2:2.45	0/0:1:2.20	0/0:3:2.80	0/0:5:3.40

public/testdata/NA12878.chr1_10mb_11mb.slx.indels.vcf4

@@ -1,5 +0,0 @@
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-1	10075180	.	G	GAAAAG	.	PASS	.	GT	1/0
-1	10093647	.	CTCT	C	.	PASS	.	GT	1/0
-1	10271352	.	G	GTTTT	.	PASS	.	GT	1/0

public/testdata/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf

@@ -1,243 +0,0 @@
-##fileformat=VCFv4.0
-##FILTER=<ID=ABFilter,Description="AB  0.75 && DP  40">
-##FILTER=<ID=DPFilter,Description="DP  120 || SB  -0.10">
-##FILTER=<ID=FDRtranche0.00to0.10,Description="FDR tranche level at qual 0.06">
-##FILTER=<ID=FDRtranche0.10to1.00,Description="FDR tranche level at qual 0.03">
-##FILTER=<ID=FDRtranche1.00to2.00,Description="FDR tranche level at qual 0.02">
-##FILTER=<ID=FDRtranche2.00to10.00+,Description="FDR tranche level at qual  0.06">
-##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 = 4 && ((MQ0 / (1.0 * DP))  0.1)">
-##FILTER=<ID=Indel,Description="Overlaps a user-input mask">
-##FILTER=<ID=LowQual,Description="Low quality">
-##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FilterLiftedVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/tmp/0.069557317373441.sorted.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=FilterLiftedVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
-##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
-##LiftoverVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/home/radon01/kiran/scr1/projects/DataProcessingPaper/results/newForStacey/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=LiftoverVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub chain=/humgen/gsa-hpprojects/GATK/data/Liftover_Chain_Files/hg18ToHg19.broad.over.chain newSequenceDictionary=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dict"
-##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:10000000-10100000] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false"
-##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-23/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-24/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-5/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-9/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-6/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-19/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-25/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-4/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-14/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-22/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-2/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-3/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-7/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-16/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-1/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-17/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-8/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-10/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-18/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-20/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-11/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-15/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-21/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-12/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-13/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam] read_buffer_size=null read_filter=[] intervals=[chrX] excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod, interval,Intervals,chrX] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod hapmap=null hapmap_chip=null out=null err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=10000 num_threads=1 interval_merging=ALL read_group_black_list=null genotype_model=JOINT_ESTIMATE base_model=EMPIRICAL heterozygosity=7.8E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null platform=null min_base_quality_score=20 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 cap_base_quality_by_mapping_quality=false"
-##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf, mask,Bed,wgs.v9/HiSeq.WGS.cleaned.indels.10.mask] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Indel NO_HEADER=false"
-##source=SelectVariants
-##source=VariantOptimizer
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10000117	rs4816203	C	T	77.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=867.45;QD=13.77;SB=-268.09	GT:AD:DP:GL:GQ	0/1:36,27:63:-109.01,-18.98,-129.63:99
-20	10000211	rs4813908	C	T	273.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.66;MQ0=0;OQ=913.43;QD=16.61;SB=-383.86	GT:AD:DP:GL:GQ	0/1:28,27:53:-110.59,-15.96,-95.89:99
-20	10000439	rs4816204	T	G	489.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=2354.98;QD=29.44;SB=-1083.04	GT:AD:DP:GL:GQ	1/1:0,80:77:-239.15,-23.21,-0.06:99
-20	10000598	rs6057087	T	A	659.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.58;MQ0=0;OQ=1772.11;QD=36.92;SB=-761.69	GT:AD:DP:GL:GQ	1/1:0,48:48:-180.81,-14.46,-0.01:99
-20	10000694	rs6057088	G	A	276.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=49.18;MQ0=0;OQ=1128.96;QD=14.11;SB=-510.63	GT:AD:DP:GL:GQ	0/1:46,34:80:-140.27,-24.09,-169.48:99
-20	10000758	rs6057089	T	A	243.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.23;MQ0=0;OQ=3541.99;QD=38.92;SB=-1671.36	GT:AD:DP:GL:GQ	1/1:0,91:91:-353.20,-27.40,-0.02:99
-20	10001019	rs6077626	T	G	401.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.70;MQ0=2;OQ=712.45;QD=10.33;SB=-352.52	GT:AD:DP:GL:GQ	0/1:40,29:65:-94.10,-19.57,-146.27:99
-20	10001298	rs1535165	T	A	637.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.34;MQ0=0;OQ=2708.88;QD=36.61;SB=-1143.40	GT:AD:DP:GL:GQ	1/1:0,73:73:-274.49,-21.99,-0.02:99
-20	10001474	rs1535166	C	T	608.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.97;MQ0=0;OQ=2678.14;QD=38.26;SB=-1011.68	GT:AD:DP:GL:GQ	1/1:0,70:69:-271.42,-20.79,-0.02:99
-20	10001617	rs2876191	C	A	279.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.17;MQ0=0;OQ=1439.09;QD=14.25;SB=-481.71	GT:AD:DP:GL:GQ	0/1:52,49:101:-177.61,-30.42,-186.45:99
-20	10001628	rs1535167	G	A	101.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.36;MQ0=0;OQ=3780.26;QD=40.22;SB=-1550.04	GT:AD:DP:GL:GQ	1/1:0,93:93:-377.03,-30.13,-2.37:99
-20	10001661	rs1535168	T	C	621.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.09;MQ0=0;OQ=2787.58;QD=34.41;SB=-1177.74	GT:AD:DP:GL:GQ	1/1:0,81:79:-282.37,-23.79,-0.02:99
-20	10001670	rs1535169	T	G	512.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.21;MQ0=0;OQ=2852.67;QD=35.22;SB=-1272.32	GT:AD:DP:GL:GQ	1/1:0,81:80:-288.87,-24.09,-0.02:99
-20	10002058	rs4404352	T	G	305.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.60;MQ0=0;OQ=2628.53;QD=34.14;SB=-934.22	GT:AD:DP:GL:GQ	1/1:1,76:75:-266.46,-22.59,-0.03:99
-20	10002099	rs4555427	C	T	2.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=5;HaplotypeScore=0.47;MQ=56.02;MQ0=0;OQ=1117.99;QD=17.47;SB=-498.13	GT:AD:DP:GL:GQ	0/1:27,37:61:-133.46,-18.38,-95.58:99
-20	10002138	rs4569544	C	G	481.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.30;MQ0=0;OQ=2204.77;QD=40.09;SB=-1043.64	GT:AD:DP:GL:GQ	1/1:0,55:51:-224.08,-15.37,-0.01:99
-20	10002142	rs4417777	G	C	579.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=2117.84;QD=39.22;SB=-975.74	GT:AD:DP:GL:GQ	1/1:0,54:49:-215.38,-14.76,-0.01:99
-20	10002470	rs2327260	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=11;HaplotypeScore=1.75;MQ=47.38;MQ0=0;OQ=2328.93;QD=34.25;SB=-1076.99	GT:AD:DP:GL:GQ	1/1:0,68:61:-236.50,-18.38,-0.02:99
-20	10002478	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=7;HaplotypeScore=9.60;MQ=53.59;MQ0=0;OQ=111.85;QD=2.00;SB=59.21	GT:AD:DP:GL:GQ	0/1:47,9:46:-28.33,-13.86,-140.18:99
-20	10002625	rs2144570	G	T	624.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.02;MQ0=0;OQ=2238.72;QD=36.11;SB=-983.67	GT:AD:DP:GL:GQ	1/1:0,62:61:-227.47,-18.37,-0.01:99
-20	10003021	rs6057090	C	T	599.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2357.20;QD=38.64;SB=-1005.68	GT:AD:DP:GL:GQ	1/1:0,61:60:-239.32,-18.08,-0.02:99
-20	10003358	rs926982	A	C	283.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=1239.40;QD=14.58;SB=-411.81	GT:AD:DP:GL:GQ	0/1:43,42:84:-152.52,-25.30,-151.13:99
-20	10003651	rs926984	T	C	632.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=3208.86;QD=35.65;SB=-1068.08	GT:AD:DP:GL:GQ	1/1:0,90:89:-324.50,-26.81,-0.03:99
-20	10003692	rs2064653	A	G	614.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=2247.29;QD=34.05;SB=-940.96	GT:AD:DP:GL:GQ	1/1:0,66:65:-228.34,-19.58,-0.03:99
-20	10003832	rs6057091	G	A	453.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.79;MQ0=0;OQ=2581.24;QD=40.33;SB=-971.37	GT:AD:DP:GL:GQ	1/1:0,64:64:-261.72,-19.28,-0.01:99
-20	10004094	rs1988590	A	C	5.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=53.93;MQ0=0;OQ=1571.64;QD=30.82;SB=-600.05	GT:AD:DP:GL:GQ	1/1:0,51:46:-160.77,-13.86,-0.02:99
-20	10004147	rs1988591	A	G	22.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.77;MQ=56.98;MQ0=0;OQ=1621.26;QD=30.59;SB=-586.00	GT:AD:DP:GL:GQ	1/1:0,53:50:-165.75,-15.08,-0.04:99
-20	10004193	.	G	T	112	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.87;MQ0=0;OQ=817.22;QD=15.13;SB=-391.14	GT:AD:DP:GL:GQ	0/1:25,29:51:-100.37,-15.36,-82.85:99
-20	10004351	rs6057092	C	G	541.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2906.33;QD=42.74;SB=-1364.94	GT:AD:DP:GL:GQ	1/1:0,68:67:-294.24,-20.19,-0.02:99
-20	10004389	rs6057093	T	G	609.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.09;MQ0=0;OQ=2210.27;QD=35.65;SB=-884.11	GT:AD:DP:GL:GQ	1/1:0,62:62:-224.63,-18.68,-0.02:99
-20	10004610	rs2064654	A	C	2.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=10.08;MQ=58.45;MQ0=0;OQ=3199.99;QD=35.56;SB=-1545.20	GT:AD:DP:GL:GQ	1/1:1,89:88:-323.60,-26.50,-0.02:99
-20	10004725	rs10485737	A	G	457.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.27;MQ0=0;OQ=850.43;QD=13.08;SB=-367.17	GT:AD:DP:GL:GQ	0/1:35,30:65:-107.90,-19.58,-141.57:99
-20	10004874	rs725567	A	C	315.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.30;MQ0=0;OQ=2956.73;QD=35.20;SB=-1190.16	GT:AD:DP:GL:GQ	1/1:0,84:83:-299.28,-25.00,-0.02:99
-20	10004887	rs725566	A	G	256.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=59.44;MQ0=0;OQ=1129.32;QD=13.61;SB=-455.56	GT:AD:DP:GL:GQ	0/1:44,39:82:-140.92,-24.70,-171.36:99
-20	10005010	rs725565	C	T	706.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2824.42;QD=39.23;SB=-1089.38	GT:AD:DP:GL:GQ	1/1:0,72:71:-286.04,-21.39,-0.02:99
-20	10005427	rs6057094	C	T	587.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2155.03;QD=39.91;SB=-1081.37	GT:AD:DP:GL:GQ	1/1:0,54:54:-219.10,-16.26,-0.01:99
-20	10005499	rs6077631	A	G	634.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2607.55;QD=35.72;SB=-1078.12	GT:AD:DP:GL:GQ	1/1:0,73:73:-264.36,-21.99,-0.02:99
-20	10005587	rs6108375	A	G	498.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1061.48;QD=14.95;SB=-522.04	GT:AD:DP:GL:GQ	0/1:35,36:70:-130.52,-21.08,-138.09:99
-20	10005723	rs6108376	A	G	529.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2687.35;QD=31.62;SB=-1283.54	GT:AD:DP:GL:GQ	1/1:0,85:83:-272.38,-25.03,-0.06:99
-20	10006291	rs6118856	G	A	172.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.54;MQ0=0;OQ=908.18;QD=11.08;SB=-459.38	GT:AD:DP:GL:GQ	0/1:53,29:82:-118.80,-24.70,-191.13:99
-20	10006404	rs926985	A	C	490.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=2586.62;QD=33.59;SB=-921.26	GT:AD:DP:GL:GQ	1/1:0,77:75:-262.28,-22.59,-0.03:99
-20	10006682	rs6057095	T	A	131.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.43;MQ0=0;OQ=2662.92;QD=36.48;SB=-986.49	GT:AD:DP:GL:GQ	1/1:0,72:71:-269.90,-21.39,-0.02:99
-20	10007150	rs11904989	G	C	276.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.70;MQ0=0;OQ=742.20;QD=11.78;SB=-296.80	GT:AD:DP:GL:GQ	0/1:38,25:60:-95.59,-18.09,-157.44:99
-20	10007175	rs2207850	C	T	90.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.69;MQ0=0;OQ=1294.38;QD=21.22;SB=-604.18	GT:AD:DP:GL:GQ	0/1:22,39:58:-150.19,-17.47,-75.88:99
-20	10007352	rs1884399	C	T	614.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2708.19;QD=39.25;SB=-1162.02	GT:AD:DP:GL:GQ	1/1:0,69:68:-274.43,-20.49,-0.02:99
-20	10007531	rs1884400	A	G	493.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2611.60;QD=36.78;SB=-843.33	GT:AD:DP:GL:GQ	1/1:0,71:71:-264.76,-21.38,-0.02:99
-20	10007980	rs2876192	A	C	668.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.73;MQ0=0;OQ=3022.49;QD=34.35;SB=-1434.18	GT:AD:DP:GL:GQ	1/1:0,88:87:-305.86,-26.20,-0.03:99
-20	10008221	rs2876193	T	C	510.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.18;MQ0=0;OQ=2840.34;QD=36.41;SB=-1397.57	GT:AD:DP:GL:GQ	1/1:0,78:78:-287.64,-23.49,-0.02:99
-20	10008458	rs6087107	T	G	157.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=52.94;MQ0=0;OQ=2398.43;QD=33.78;SB=-1015.12	GT:AD:DP:GL:GQ	1/1:0,71:68:-243.45,-20.48,-0.02:99
-20	10008742	rs12479925	G	T	146.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=35.86;MQ0=1;OQ=685.54;QD=12.24;SB=-274.47	GT:AD:DP:GL:GQ	0/1:26,30:43:-84.79,-12.96,-61.80:99
-20	10008951	.	A	C	553.29	Indel	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=16.13;MQ=51.15;MQ0=0;QD=11.77;SB=-184.92	GT:AD:DP:GL:GQ	0/1:23,24:43:-71.58,-12.97,-70.23:99
-20	10009227	rs12481420	A	G	523.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=1201.44;QD=19.70;SB=-625.90	GT:AD:DP:GL:GQ	0/1:22,39:61:-141.80,-18.37,-90.52:99
-20	10009246	rs4574174	A	G	634.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.62;MQ0=0;OQ=2711.91;QD=35.68;SB=-1179.49	GT:AD:DP:GL:GQ	1/1:0,76:75:-274.80,-22.59,-0.02:99
-20	10009400	rs6057096	T	A	7.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2788.17;QD=38.19;SB=-1314.62	GT:AD:DP:GL:GQ	1/1:0,73:73:-282.42,-21.98,-0.01:99
-20	10009512	rs6039657	C	G	565.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.53;MQ0=0;OQ=3160.94;QD=41.59;SB=-1228.86	GT:AD:DP:GL:GQ	1/1:0,76:74:-319.70,-22.30,-0.02:99
-20	10009719	rs6057097	A	G	58.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.33;MQ0=0;OQ=1551.35;QD=25.02;SB=-585.82	GT:AD:DP:GL:GQ	1/1:0,62:50:-158.78,-15.09,-0.06:99
-20	10009795	rs6118861	A	G	501.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1594.00;QD=35.42;SB=-578.40	GT:AD:DP:GL:GQ	1/1:0,45:45:-163.00,-13.55,-0.01:99
-20	10009844	rs6057098	G	A	11.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.92;MQ=52.80;MQ0=0;OQ=1658.97;QD=30.16;SB=-750.39	GT:AD:DP:GL:GQ	0/1:8,47:51:-184.54,-15.37,-17.54:21.74
-20	10009871	rs6133780	A	G	1067.52	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=16.85;MQ=51.54;MQ0=0;QD=18.09;SB=-387.29	GT:AD:DP:GL:GQ	0/1:19,40:49:-124.80,-14.77,-52.03:99
-20	10009875	rs6133781	A	G	1106.95	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=19.06;MQ=51.21;MQ0=0;QD=19.42;SB=-410.34	GT:AD:DP:GL:GQ	0/1:16,41:44:-127.23,-13.25,-35.68:99
-20	10009879	.	A	G	1218.05	SnpCluster	AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;HRun=1;HaplotypeScore=20.77;MQ=51.40;MQ0=0;QD=23.88;SB=-543.65	GT:AD:DP:GL:GQ	1/1:5,46:42:-136.91,-12.65,-11.59:10.59
-20	10009883	rs6133782	A	G	1399.75	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=11.88;MQ=52.16;MQ0=0;QD=27.45;SB=-484.45	GT:AD:DP:GL:GQ	1/1:2,49:43:-147.73,-12.95,-4.17:87.80
-20	10010393	rs513998	T	G	602.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=1247.20;QD=16.20;SB=-518.70	GT:AD:DP:GL:GQ	0/1:35,42:76:-150.89,-22.89,-128.62:99
-20	10010766	rs517531	T	G	421.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2100.93;QD=31.36;SB=-978.12	GT:AD:DP:GL:GQ	1/1:0,66:67:-217.39,-23.46,-3.72:99
-20	10010832	rs582827	T	C	733.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=2668.46;QD=35.58;SB=-1048.08	GT:AD:DP:GL:GQ	1/1:0,75:75:-270.45,-22.59,-0.02:99
-20	10011075	rs6039659	C	T	234.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=60.00;MQ0=0;OQ=1322.11;QD=15.74;SB=-644.72	GT:AD:DP:GL:GQ	0/1:45,39:82:-160.20,-24.71,-141.60:99
-20	10011309	rs641722	T	C	546.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=2396.22;QD=30.72;SB=-1026.41	GT:AD:DP:GL:GQ	1/1:0,78:76:-243.28,-22.92,-0.07:99
-20	10011666	rs546821	C	T	285.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2849.79;QD=40.14;SB=-1187.35	GT:AD:DP:GL:GQ	1/1:0,71:71:-288.58,-21.39,-0.02:99
-20	10011939	rs548863	C	T	181.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=56.14;MQ0=0;OQ=2488.04;QD=39.49;SB=-885.19	GT:AD:DP:GL:GQ	1/1:0,63:62:-252.40,-18.68,-0.01:99
-20	10012362	rs574425	G	T	17.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=51.41;MQ0=0;OQ=676.99;QD=28.21;SB=-89.90	GT:AD:DP:GL:GQ	1/1:0,24:20:-71.29,-6.02,-0.01:60.18
-20	10012384	rs7270107	T	C	128.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=51.62;MQ0=0;OQ=216.13;QD=12.01;SB=-75.35	GT:AD:DP:GL:GQ	0/1:9,9:16:-29.72,-4.82,-34.04:99
-20	10012387	rs6057102	T	C	18.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=50.47;MQ0=0;OQ=295.02;QD=18.44;SB=-77.36	GT:AD:DP:GL:GQ	1/1:0,16:11:-33.10,-3.32,-0.02:33.06
-20	10012479	rs575394	A	G	3.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=49.52;MQ0=0;OQ=474.16;QD=23.71;SB=-247.57	GT:AD:DP:GL:GQ	1/1:0,20:16:-51.02,-4.83,-0.02:48.10
-20	10012498	rs657453	C	G	2.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=40.06;MQ0=0;OQ=331.25;QD=22.08;SB=-84.82	GT:AD:DP:GL:GQ	1/1:0,15:9:-36.71,-2.71,-0.01:27.09
-20	10012518	rs657490	T	C	1.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.64;MQ=34.32;MQ0=0;OQ=366.95;QD=22.93;SB=-197.06	GT:AD:DP:GL:GQ	1/1:0,16:12:-40.29,-3.62,-0.01:36.09
-20	10012521	rs6141099	C	T	33.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=35.97;MQ0=0;OQ=104.02;QD=5.78;SB=-64.27	GT:AD:DP:GL:GQ	0/1:11,7:14:-17.91,-4.23,-28.63:99
-20	10012636	rs57357029	G	C	442.35	Indel	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=3;HaplotypeScore=2.47;MQ=46.22;MQ0=1;QD=17.69;SB=-127.71	GT:AD:DP:GL:GQ	0/1:10,15:20:-53.56,-6.04,-26.16:99
-20	10012714	rs577258	G	C	4.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=54.18;MQ0=0;OQ=1374.69;QD=38.19;SB=-268.50	GT:AD:DP:GL:GQ	1/1:0,36:34:-141.07,-10.25,-0.02:99
-20	10012751	rs577383	T	C	3.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=51.17;MQ0=0;OQ=807.71;QD=26.06;SB=-389.47	GT:AD:DP:GL:GQ	1/1:0,31:26:-84.38,-7.84,-0.03:78.14
-20	10013119	rs670350	C	T	14.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.14;MQ=53.67;MQ0=0;OQ=1037.37;QD=17.58;SB=-503.12	GT:AD:DP:GL:GQ	0/1:27,32:57:-124.19,-17.17,-93.21:99
-20	10013574	rs6057108	G	A	190.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.43;MQ0=0;OQ=995.08;QD=15.08;SB=-284.14	GT:AD:DP:GL:GQ	0/1:36,30:66:-122.67,-19.88,-129.26:99
-20	10015679	.	C	T	4.66	PASS	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=130.84;QD=11.89;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,6:10:-19.38,-3.01,-17.14:99
-20	10015761	rs12106014	T	C	188.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=282.39;QD=12.84;SB=-35.94	GT:AD:DP:GL:GQ	0/1:9,13:21:-37.85,-6.33,-34.21:99
-20	10018158	rs512313	G	C	152.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.79;MQ0=0;OQ=1786.48;QD=20.53;SB=-749.98	GT:AD:DP:GL:GQ	0/1:39,47:85:-207.56,-25.63,-151.93:99
-20	10018555	rs570855	G	A	501.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1507.16;QD=18.61;SB=-748.62	GT:AD:DP:GL:GQ	0/1:36,45:80:-178.09,-24.09,-134.36:99
-20	10019093	rs575534	A	G	198.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=59.34;MQ0=0;OQ=1097.34;QD=15.68;SB=-511.28	GT:AD:DP:GL:GQ	0/1:34,36:69:-133.80,-20.78,-132.32:99
-20	10020229	rs596203	G	A	334.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.76;MQ0=0;OQ=1448.48;QD=18.34;SB=-632.66	GT:AD:DP:GL:GQ	0/1:37,42:79:-171.94,-23.81,-120.12:99
-20	10023689	rs4813909	G	A	153.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.04;MQ0=0;OQ=1887.80;QD=22.74;SB=-948.03	GT:AD:DP:GL:GQ	0/1:30,53:83:-217.06,-25.00,-110.51:99
-20	10024107	.	C	T	114.08	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.56;MQ0=0;OQ=1618.74;QD=19.04;SB=-735.06	GT:AD:DP:GL:GQ	0/1:38,47:84:-190.47,-25.31,-121.49:99
-20	10024288	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=5;HaplotypeScore=7.93;MQ=51.94;MQ0=0;OQ=68.97;QD=0.97;SB=86.23	GT:AD:DP:GL:GQ	0/1:53,18:57:-27.36,-17.18,-167.04:99
-20	10024294	.	C	T	19.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=5;HaplotypeScore=23.45;MQ=49.01;MQ0=1;QD=0.27;SB=83.26	GT:AD:DP:GL:GQ	0/1:55,18:51:-20.62,-15.37,-156.17:52.53
-20	10026357	rs685723	T	C	589.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1010.93;QD=16.57;SB=-474.08	GT:AD:DP:GL:GQ	0/1:26,35:60:-122.45,-18.07,-104.85:99
-20	10026794	rs687514	C	T	152.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=60.00;MQ0=0;OQ=1015.27;QD=19.52;SB=-447.00	GT:AD:DP:GL:GQ	0/1:19,32:49:-119.58,-14.77,-61.54:99
-20	10027868	rs514832	A	G	410.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.47;MQ0=0;OQ=1149.09;QD=13.21;SB=-556.55	GT:AD:DP:GL:GQ	0/1:43,44:87:-144.42,-26.22,-173.75:99
-20	10027872	rs594811	A	G	112.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.44;MQ0=0;OQ=1351.31;QD=16.28;SB=-565.56	GT:AD:DP:GL:GQ	0/1:39,44:83:-163.41,-25.00,-161.96:99
-20	10030188	rs652633	T	A	473.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.71;MQ0=0;OQ=1186.53;QD=15.02;SB=-453.42	GT:AD:DP:GL:GQ	0/1:41,38:79:-145.73,-23.79,-157.38:99
-20	10031342	rs668091	G	A	109.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=60.00;MQ0=0;OQ=1739.31;QD=19.11;SB=-748.28	GT:AD:DP:GL:GQ	0/1:41,50:90:-204.32,-27.11,-145.56:99
-20	10031798	rs669985	G	A	353.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=4247.21;QD=40.84;SB=-1915.55	GT:AD:DP:GL:GQ	1/1:0,104:104:-423.72,-31.33,-0.03:99
-20	10031827	rs558493	C	T	27.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.83;MQ0=0;OQ=1957.26;QD=18.12;SB=-1004.58	GT:AD:DP:GL:GQ	0/1:52,56:108:-231.54,-32.53,-189.42:99
-20	10032094	rs681750	G	A	562.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.21;QD=14.16;SB=-575.44	GT:AD:DP:GL:GQ	0/1:47,36:82:-145.51,-24.71,-151.92:99
-20	10032413	rs683145	T	G	535.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=698.84;QD=11.09;SB=-317.98	GT:AD:DP:GL:GQ	0/1:33,30:63:-92.15,-18.98,-124.49:99
-20	10032882	rs479039	A	T	24.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.01;HRun=0;HaplotypeScore=7.14;MQ=58.99;MQ0=0;OQ=1029.41;QD=13.73;SB=-439.55	GT:AD:DP:GL:GQ	0/1:40,34:73:-128.21,-21.99,-155.80:99
-20	10034306	rs604452	T	C	170.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=59.46;MQ0=0;OQ=667.43;QD=8.67;SB=-359.16	GT:AD:DP:GL:GQ	0/1:47,29:73:-92.02,-22.00,-181.63:99
-20	10037037	rs2327261	C	T	271.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.97;MQ0=0;OQ=1384.69;QD=17.53;SB=-468.51	GT:AD:DP:GL:GQ	0/1:38,41:74:-164.05,-22.30,-111.89:99
-20	10037709	rs518364	A	T	403.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.68;MQ0=0;OQ=896.68;QD=12.63;SB=-381.55	GT:AD:DP:GL:GQ	0/1:39,32:70:-114.04,-21.09,-148.36:99
-20	10039371	rs678696	T	G	586.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1105.57;QD=15.79;SB=-406.66	GT:AD:DP:GL:GQ	0/1:32,38:70:-134.92,-21.08,-120.34:99
-20	10040821	rs6057119	T	A	1156.74	Indel	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.03;HRun=6;HaplotypeScore=36.61;MQ=50.69;MQ0=0;QD=15.22;SB=-511.29	GT:AD:DP:GL:GQ	0/1:35,39:75:-140.95,-21.99,-129.69:99
-20	10041304	rs559129	C	T	83.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.92;MQ=59.66;MQ0=0;OQ=2692.91;QD=39.60;SB=-1319.36	GT:AD:DP:GL:GQ	1/1:0,68:67:-272.89,-20.18,-0.01:99
-20	10042319	rs631317	C	T	711.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.00;MQ0=0;OQ=2553.65;QD=39.29;SB=-1137.05	GT:AD:DP:GL:GQ	1/1:0,65:64:-258.97,-19.28,-0.02:99
-20	10042761	rs633445	A	G	631.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3233.06;QD=35.53;SB=-1142.81	GT:AD:DP:GL:GQ	1/1:0,91:88:-327.18,-26.51,-0.02:99
-20	10042829	rs633841	A	G	305.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.76;MQ0=0;OQ=2746.23;QD=35.21;SB=-1237.83	GT:AD:DP:GL:GQ	1/1:0,78:77:-278.24,-23.20,-0.03:99
-20	10043002	.	A	T	147.57	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1103.68;QD=13.14;SB=-535.28	GT:AD:DP:GL:GQ	0/1:48,36:84:-138.95,-25.30,-175.62:99
-20	10044849	rs663380	A	G	242.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1840.58;QD=31.20;SB=-654.96	GT:AD:DP:GL:GQ	1/1:0,59:57:-187.68,-17.18,-0.04:99
-20	10045078	rs674630	G	T	86.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=1.98;MQ=58.99;MQ0=0;OQ=2874.89;QD=36.39;SB=-1368.13	GT:AD:DP:GL:GQ	1/1:0,79:78:-291.09,-23.49,-0.02:99
-20	10045642	rs572752	G	C	658.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3374.18;QD=42.18;SB=-1455.16	GT:AD:DP:GL:GQ	1/1:0,80:79:-336.42,-23.81,-0.03:99
-20	10046537	rs583827	A	G	86.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.76;MQ=54.17;MQ0=0;OQ=719.43;QD=12.40;SB=-246.31	GT:AD:DP:GL:GQ	0/1:29,29:55:-91.80,-16.57,-108.67:99
-20	10050828	rs660454	T	C	314.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.73;MQ0=0;OQ=1072.85;QD=12.62;SB=-513.86	GT:AD:DP:GL:GQ	0/1:48,37:84:-135.87,-25.30,-193.36:99
-20	10051448	rs565455	T	C	358.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=59.41;MQ0=0;OQ=1005.69;QD=14.16;SB=-400.33	GT:AD:DP:GL:GQ	0/1:36,35:69:-124.64,-20.79,-133.98:99
-20	10052688	.	C	A	247.91	PASS	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=928.77;QD=12.06;SB=-460.78	GT:AD:DP:GL:GQ	0/1:45,32:77:-119.35,-23.19,-165.26:99
-20	10058022	rs531797	T	C	82.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=6.22;MQ=58.46;MQ0=0;OQ=872.91;QD=12.47;SB=-339.92	GT:AD:DP:GL:GQ	0/1:38,32:67:-110.76,-20.18,-144.54:99
-20	10067090	rs507568	C	A	124.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=55.67;MQ0=0;OQ=1789.54;QD=33.76;SB=-802.84	GT:AD:DP:GL:GQ	1/1:0,53:50:-182.55,-15.06,-0.02:99
-20	10067264	rs530271	G	A	217.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.68;MQ0=0;OQ=2865.42;QD=39.80;SB=-1324.28	GT:AD:DP:GL:GQ	1/1:0,72:72:-290.15,-21.69,-0.02:99
-20	10067722	rs604416	A	C	278.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1822.34;QD=35.05;SB=-862.09	GT:AD:DP:GL:GQ	1/1:0,52:52:-185.83,-15.66,-0.02:99
-20	10068981	rs490505	G	A	49.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=1.07;MQ=59.55;MQ0=0;OQ=2469.03;QD=39.82;SB=-1135.04	GT:AD:DP:GL:GQ	1/1:0,62:61:-250.50,-18.37,-0.01:99
-20	10070602	rs6039684	T	C	187.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.71;MQ0=0;OQ=2364.76;QD=32.84;SB=-1139.10	GT:AD:DP:GL:GQ	1/1:0,72:69:-240.09,-20.79,-0.03:99
-20	10070936	.	T	A	3050.87	Indel	AC=2;AF=1.00;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=2.65;MQ=58.76;MQ0=0;QD=37.67;SB=-1399.42	GT:AD:DP:GL:GQ	1/1:0,81:80:-308.69,-24.09,-0.02:99
-20	10071135	rs552048	C	T	173.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=59.09;MQ0=0;OQ=3089.23;QD=40.65;SB=-1301.70	GT:AD:DP:GL:GQ	1/1:0,76:76:-312.53,-22.89,-0.02:99
-20	10071187	rs6032780	G	A	696.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=3367.02;QD=40.57;SB=-1247.04	GT:AD:DP:GL:GQ	1/1:0,83:82:-335.70,-24.70,-0.02:99
-20	10071890	rs6039685	T	C	547.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1748.72;QD=30.68;SB=-861.55	GT:AD:DP:GL:GQ	1/1:0,57:56:-178.51,-16.89,-0.05:99
-20	10072505	rs6032786	A	G	465.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1789.94;QD=28.41;SB=-916.44	GT:AD:DP:GL:GQ	1/1:0,63:57:-182.63,-17.19,-0.05:99
-20	10074187	.	A	G	68.82	PASS	AC=2;AF=1.00;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=2702.25;QD=35.09;SB=-1331.57	GT:AD:DP:GL:GQ	1/1:0,77:77:-273.84,-23.20,-0.03:99
-20	10074240	rs614270	T	C	574.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2989.29;QD=34.76;SB=-1439.46	GT:AD:DP:GL:GQ	1/1:0,85:83:-302.53,-25.00,-0.02:99
-20	10074716	rs2327236	G	A	207.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=2351.97;QD=35.10;SB=-934.35	GT:AD:DP:GL:GQ	1/1:0,67:62:-238.81,-18.69,-0.03:99
-20	10074806	rs2327237	G	A	618.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2806.22;QD=38.98;SB=-1369.05	GT:AD:DP:GL:GQ	1/1:0,72:71:-284.22,-21.39,-0.02:99
-20	10075043	rs617891	T	C	295.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2170.63;QD=35.58;SB=-943.96	GT:AD:DP:GL:GQ	1/1:0,61:61:-220.67,-18.37,-0.02:99
-20	10075168	rs6032787	C	T	590.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=3524.41;QD=40.05;SB=-1505.51	GT:AD:DP:GL:GQ	1/1:0,88:86:-351.44,-25.90,-0.02:99
-20	10076250	rs644043	A	G	293.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.71;MQ0=0;OQ=915.84;QD=11.59;SB=-456.82	GT:AD:DP:GL:GQ	0/1:41,38:77:-118.08,-23.21,-160.58:99
-20	10076339	rs644160	A	G	242.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=59.35;MQ0=0;OQ=1102.11;QD=15.52;SB=-557.03	GT:AD:DP:GL:GQ	0/1:33,38:71:-134.88,-21.39,-128.30:99
-20	10076399	rs506458	G	A	360.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1756.48;QD=18.69;SB=-796.27	GT:AD:DP:GL:GQ	0/1:44,50:94:-207.24,-28.31,-163.43:99
-20	10077752	.	T	C	195.33	PASS	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1175.95;QD=14.89;SB=-463.61	GT:AD:DP:GL:GQ	0/1:34,45:79:-144.69,-23.81,-137.94:99
-20	10081750	rs473369	C	A	178.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1188.67;QD=14.50;SB=-583.96	GT:AD:DP:GL:GQ	0/1:43,39:82:-146.85,-24.69,-154.74:99
-20	10081800	rs474169	C	T	600.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1088.62;QD=16.25;SB=-544.01	GT:AD:DP:GL:GQ	0/1:34,33:67:-132.33,-20.18,-122.19:99
-20	10082892	rs644145	C	T	208.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=1601.32;QD=38.13;SB=-762.50	GT:AD:DP:GL:GQ	1/1:0,42:41:-163.73,-12.35,-0.01:99
-20	10085211	rs685573	A	T	447.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.51;MQ0=0;OQ=1024.78;QD=13.48;SB=-509.23	GT:AD:DP:GL:GQ	0/1:42,34:75:-128.35,-22.59,-157.06:99
-20	10086110	rs592026	G	A	451.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.14;MQ0=0;OQ=1254.60;QD=15.49;SB=-639.16	GT:AD:DP:GL:GQ	0/1:43,38:81:-153.14,-24.40,-157.02:99
-20	10086283	rs592889	G	T	230.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=882.77;QD=10.51;SB=-462.82	GT:AD:DP:GL:GQ	0/1:52,32:84:-116.86,-25.30,-180.39:99
-20	10086619	rs513535	T	A	1.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=5;HaplotypeScore=1.00;MQ=59.68;MQ0=0;OQ=746.98;QD=10.52;SB=-282.61	GT:AD:DP:GL:GQ	0/1:45,26:69:-98.76,-20.78,-164.07:99
-20	10086853	rs127733	G	A	343.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.75;MQ0=0;OQ=945.98;QD=12.78;SB=-472.45	GT:AD:DP:GL:GQ	0/1:42,32:71:-119.28,-21.40,-133.60:99
-20	10086954	rs595987	G	A	578.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1076.10;QD=16.06;SB=-401.89	GT:AD:DP:GL:GQ	0/1:33,34:66:-130.79,-19.89,-110.09:99
-20	10087230	rs607331	A	G	497.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=1624.42;QD=17.10;SB=-744.63	GT:AD:DP:GL:GQ	0/1:41,54:95:-194.34,-28.62,-167.75:99
-20	10087394	rs608188	T	G	410.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.72;MQ0=0;OQ=1428.70;QD=17.21;SB=-695.70	GT:AD:DP:GL:GQ	0/1:35,48:83:-171.15,-25.00,-131.95:99
-20	10087754	rs544718	T	G	209.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=60.45;MQ0=0;OQ=1195.66;QD=15.33;SB=-504.83	GT:AD:DP:GL:GQ	0/1:36,42:77:-146.04,-23.19,-131.14:99
-20	10087804	rs609932	C	T	337.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=60.49;MQ0=0;OQ=1534.51;QD=15.35;SB=-666.41	GT:AD:DP:GL:GQ	0/1:50,50:93:-184.76,-28.03,-153.45:99
-20	10088063	rs621673	C	T	498.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.79;MQ0=0;OQ=1322.79;QD=15.20;SB=-531.00	GT:AD:DP:GL:GQ	0/1:46,41:84:-160.88,-25.32,-143.12:99
-20	10088699	rs498420	C	T	139.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.78;MQ=54.80;MQ0=0;OQ=803.84;QD=12.18;SB=-217.49	GT:AD:DP:GL:GQ	0/1:38,28:61:-102.06,-18.39,-112.29:99
-20	10088730	rs624398	G	A	180.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=52.02;MQ0=0;OQ=706.21;QD=12.39;SB=-215.65	GT:AD:DP:GL:GQ	0/1:29,26:51:-89.27,-15.37,-99.20:99
-20	10088736	rs624401	A	C	166.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=51.41;MQ0=0;OQ=755.82;QD=12.81;SB=-289.77	GT:AD:DP:GL:GQ	0/1:29,29:53:-94.83,-15.97,-94.03:99
-20	10088747	rs624419	A	G	458.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.80;MQ0=0;OQ=732.27;QD=13.31;SB=-319.26	GT:AD:DP:GL:GQ	0/1:25,30:54:-92.79,-16.28,-99.03:99
-20	10088799	rs624824	G	A	1.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=54.24;MQ0=0;OQ=1015.57;QD=18.46;SB=-384.14	GT:AD:DP:GL:GQ	0/1:24,31:54:-121.12,-16.28,-76.29:99
-20	10088895	rs500269	C	T	289	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.39;MQ0=0;OQ=522.39;QD=12.74;SB=-237.72	GT:AD:DP:GL:GQ	0/1:24,17:39:-67.28,-11.76,-70.34:99
-20	10088985	rs2876185	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=28.26;MQ=49.95;MQ0=0;OQ=805.93;QD=10.20;SB=-330.82	GT:AD:DP:GL:GQ	0/1:43,35:73:-105.88,-22.00,-156.93:99
-20	10089441	rs637625	A	G	358.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=992.46;QD=13.23;SB=-330.00	GT:AD:DP:GL:GQ	0/1:37,38:73:-124.53,-22.00,-148.03:99
-20	10089525	rs526819	C	T	411.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.84;MQ0=0;OQ=1526.59;QD=17.96;SB=-694.71	GT:AD:DP:GL:GQ	0/1:41,44:82:-180.66,-24.71,-123.55:99
-20	10090764	rs670562	A	G	90.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=5.75;MQ=59.44;MQ0=0;OQ=705.16;QD=10.52;SB=-326.14	GT:AD:DP:GL:GQ	0/1:37,30:65:-93.39,-19.59,-148.34:99
-20	10090970	rs671426	T	C	386.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.73;MQ0=0;OQ=1093.51;QD=15.62;SB=-550.11	GT:AD:DP:GL:GQ	0/1:33,37:67:-132.81,-20.18,-125.76:99
-20	10091214	rs563455	C	T	321.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.75;MQ0=0;OQ=1276.23;QD=17.02;SB=-480.51	GT:AD:DP:GL:GQ	0/1:36,39:73:-152.90,-21.99,-128.97:99
-20	10092415	rs590717	A	G	409.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1457.26;QD=14.57;SB=-743.58	GT:AD:DP:GL:GQ	0/1:51,49:100:-179.13,-30.12,-213.26:99
-20	10092927	.	G	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=8.09;MQ=59.09;MQ0=0;OQ=102.52;QD=1.35;SB=110.34	GT:AD:DP:GL:GQ	0/1:58,17:57:-30.71,-17.17,-163.94:99
-20	10093923	rs2423481	T	A	501.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=952.53;QD=14.65;SB=-490.92	GT:AD:DP:GL:GQ	0/1:33,32:64:-117.81,-19.28,-126.25:99
-20	10094251	rs543895	T	A	466.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.29;QD=18.66;SB=-397.80	GT:AD:DP:GL:GQ	0/1:26,37:59:-138.58,-17.77,-89.00:99
-20	10094582	rs56124148	A	G	315.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.72;MQ0=0;OQ=736.10;QD=11.15;SB=-314.87	GT:AD:DP:GL:GQ	0/1:38,28:65:-96.47,-19.58,-152.04:99
-20	10094774	rs570383	C	T	361.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=1017.49;QD=13.75;SB=-374.10	GT:AD:DP:GL:GQ	0/1:39,35:69:-125.82,-20.79,-130.93:99
-20	10095741	rs489548	A	G	80.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.33;MQ=57.01;MQ0=0;OQ=943.34;QD=13.29;SB=-405.22	GT:AD:DP:GL:GQ	0/1:36,34:68:-118.10,-20.48,-142.28:99
-20	10096293	rs515940	C	T	94.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.19;MQ0=0;OQ=1320.58;QD=17.61;SB=-665.71	GT:AD:DP:GL:GQ	0/1:37,38:74:-157.63,-22.29,-130.19:99
-20	10096596	rs518701	C	T	23.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.03;MQ0=0;OQ=1543.46;QD=17.95;SB=-788.95	GT:AD:DP:GL:GQ	0/1:40,46:85:-183.24,-25.61,-136.84:99
-20	10096768	rs520453	A	C	398.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=1343.01;QD=15.44;SB=-695.73	GT:AD:DP:GL:GQ	0/1:42,45:87:-163.78,-26.20,-154.89:99
-20	10096899	rs652086	G	T	1162.66	Indel	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.76;MQ0=0;QD=14.72;SB=-335.13	GT:AD:DP:GL:GQ	0/1:39,40:78:-143.04,-23.49,-142.37:99
-20	10096933	rs652126	G	C	307.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.78;MQ0=0;OQ=1416.78;QD=16.87;SB=-379.18	GT:AD:DP:GL:GQ	0/1:45,39:83:-169.97,-25.01,-193.85:99
-20	10096958	rs652494	G	A	342.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.79;MQ0=0;OQ=1501.31;QD=16.68;SB=-462.96	GT:AD:DP:GL:GQ	0/1:45,45:87:-179.62,-26.20,-157.70:99
-20	10097075	rs6077657	T	G	299.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.69;MQ0=0;OQ=1264.80;QD=13.75;SB=-586.94	GT:AD:DP:GL:GQ	0/1:44,48:90:-156.87,-27.11,-157.64:99
-20	10097437	rs11698147	T	C	519.38	Indel	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.01;HRun=1;HaplotypeScore=8.62;MQ=55.90;MQ0=0;QD=7.75;SB=-133.24	GT:AD:DP:GL:GQ	0/1:45,21:62:-73.60,-18.38,-162.59:99
-20	10097465	.	C	T	31.87	LowQual	AC=1;AF=0.50;AN=2;DP=49;Dels=0.02;HRun=3;HaplotypeScore=12.58;MQ=57.18;MQ0=0;QD=0.61;SB=-33.97	GT:AD:DP:GL:GQ	0/1:46,5:49:-20.93,-14.46,-150.67:64.70
-20	10097626	rs665397	C	A	205.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.09;MQ0=0;OQ=521.22;QD=11.33;SB=-241.94	GT:AD:DP:GL:GQ	0/1:27,19:45:-68.96,-13.55,-93.68:99
-20	10097789	rs550824	T	C	40.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.80;MQ=57.53;MQ0=1;OQ=609.05;QD=10.15;SB=-279.29	GT:AD:DP:GL:GQ	0/1:35,25:57:-81.36,-17.17,-136.53:99
-20	10097928	rs666732	G	A	147.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=57.09;MQ0=0;OQ=647.39;QD=16.60;SB=-318.83	GT:AD:DP:GL:GQ	0/1:17,22:38:-79.48,-11.45,-61.53:99
-20	10098110	rs6108402	G	C	43.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=639.58;QD=17.77;SB=-86.92	GT:AD:DP:GL:GQ	0/1:19,17:35:-77.79,-10.55,-73.75:99
-20	10098135	rs6108403	C	A	5.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=59.93;MQ0=0;OQ=389.51;QD=10.25;SB=-43.38	GT:AD:DP:GL:GQ	0/1:24,14:38:-53.68,-11.44,-83.52:99
-20	10098237	.	A	T	39.55	PASS	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.32;MQ0=0;OQ=159.94;QD=12.30;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,6:13:-23.19,-3.92,-25.88:99
-20	10098265	.	T	C	37.58	PASS	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.10;MQ0=0;OQ=64.00;QD=12.80;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,3:5:-11.19,-1.51,-7.23:57.28
-20	10098344	.	A	G	24.50	LowQual	AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=6.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,2:4:-6.94,-1.20,-8.11:57.33
-20	10098786	.	C	T	16.33	LowQual	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=54.65;MQ0=0;QD=1.81;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,2:9:-7.62,-2.71,-21.38:49.06
-20	10098945	rs56176249	T	C	5.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=51.33;MQ0=0;OQ=363.84;QD=17.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,13:20:-45.69,-6.02,-27.59:99
-20	10098987	.	C	T	11	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.90;MQ0=0;OQ=342.06;QD=14.87;SB=-3.99	GT:AD:DP:GL:GQ	0/1:10,13:21:-43.82,-6.33,-33.84:99
-20	10099029	rs13044987	T	C	3.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.87;MQ0=0;OQ=125.69;QD=4.66;SB=2.03	GT:AD:DP:GL:GQ	0/1:18,9:25:-23.39,-7.53,-70.35:99
-20	10099034	rs13043768	C	A	139.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.19;MQ0=0;OQ=176.63;QD=6.31;SB=-31.94	GT:AD:DP:GL:GQ	0/1:18,10:26:-28.78,-7.84,-59.75:99
-20	10099044	rs13043626	A	C	29.61	LowQual	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=51.36;MQ0=0;QD=1.29;SB=-14.48	GT:AD:DP:GL:GQ	0/1:16,7:15:-10.76,-4.52,-43.68:62.44
-20	10099055	rs13045001	T	C	65.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=48.67;MQ0=0;OQ=222.63;QD=7.95;SB=-64.86	GT:AD:DP:GL:GQ	0/1:16,12:23:-32.47,-6.93,-57.23:99
-20	10099079	rs13043786	C	T	16.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=5.99;MQ=49.66;MQ0=0;OQ=370.70;QD=10.59;SB=-162.25	GT:AD:DP:GL:GQ	0/1:21,14:31:-49.70,-9.35,-56.03:99
-20	10099140	rs585009	G	T	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=5;HaplotypeScore=2.65;MQ=55.73;MQ0=0;OQ=847.58;QD=14.13;SB=-233.91	GT:AD:DP:GL:GQ	0/1:30,30:58:-105.51,-17.47,-102.15:99
-20	10099190	rs508242	G	T	210.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=57.42;MQ0=0;OQ=860.99;QD=13.25;SB=-270.28	GT:AD:DP:GL:GQ	0/1:33,32:62:-108.05,-18.67,-118.91:99
-20	10099220	rs585404	A	G	5.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=6.00;MQ=56.96;MQ0=0;OQ=481.07;QD=10.46;SB=-187.61	GT:AD:DP:GL:GQ	0/1:25,21:43:-64.35,-12.96,-100.07:99
-20	10099250	rs585439	G	A	100.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=56.23;MQ0=0;OQ=672.67;QD=17.70;SB=-330.34	GT:AD:DP:GL:GQ	0/1:17,21:36:-81.41,-10.86,-48.14:99
-20	10099535	rs586791	G	A	209.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.28;MQ0=0;OQ=1326.40;QD=20.73;SB=-582.88	GT:AD:DP:GL:GQ	0/1:25,38:62:-157.48,-21.55,-76.17:99
-20	10099565	rs532882	C	T	44.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.99;MQ=59.66;MQ0=0;OQ=1282.88;QD=19.15;SB=-617.46	GT:AD:DP:GL:GQ	0/1:30,37:67:-151.75,-20.18,-103.68:99
-20	10099755	rs534687	C	T	66.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.91;MQ=59.00;MQ0=0;OQ=1091.00;QD=16.78;SB=-547.75	GT:AD:DP:GL:GQ	0/1:32,33:64:-131.66,-19.27,-116.96:99
-20	10099832	rs534882	A	G	477.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=927.85;QD=12.89;SB=-445.10	GT:AD:DP:GL:GQ	0/1:39,33:71:-117.45,-21.39,-156.97:99

public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.FP.vcf

@@ -1,19 +0,0 @@
-##fileformat=VCFv4.0
-##PhaseByTransmissionUnitTest="This file contains only genotypes with false mendelian violations in the input data. The output data should correct the genotypes and phase the trios. The pair should be corrected and phased where possible. Genotype combination phred score should be reported where possible. The unrelated individual should remain untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_FATHER	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
-1	10109	.	A	T	99	PASS	TestDescription=HomRef/HomRef/Het	GT:GQ:PL	0/0:50:0,50,200	0/0:40:0,40,200	0/1:30:30,0,200	0/0:50:0,50,200	0/1:30:30,0,200	0/0:50:0,50,200	
-1	10147	.	C	A	99	PASS	TestDescription=HomRef/HomRef/HomAlt	GT:GQ:PL	0/0:30:0,30,200	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200	
-1	10150	.	C	T	99	PASS	TestDescription=HomRef/Het/HomAlt	GT:GQ:PL	0/0:40:0,40,200	0/1:30:30,0,200	1/1:50:200,50,0	0/0:40:0,40,200	1/1:50:200,50,0	0/0:40:0,40,200
-1	10177	.	A	C	99	PASS	TestDescription=HomRef/HomAlt/HomRef	GT:GQ:PL	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	0/0:50:0,50,200	0/0:30:0,30,200	0/0:50:0,50,200
-1	10180	.	T	C	99	PASS	TestDescription=HomRef/HomAlt/HomAlt	GT:GQ:PL	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200
-1	10234	.	C	T	99	PASS	TestDescription=Het/HomRef/HomAlt	GT:GQ:PL	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/1:40:40,0,200	1/1:50:200,50,0	0/1:40:40,0,200
-1	10235	.	T	A	99	PASS	TestDescription=Het/HomAlt/HomRef	GT:GQ:PL	0/1:50:50,0,200	1/1:40:200,40,0	0/0:30:0,30,200	0/1:50:50,0,200	0/0:30:0,30,200	0/1:50:50,0,200
-1	10236	.	A	G	99	PASS	TestDescription=HomVar/HomRef/HomRef	GT:GQ:PL	1/1:30:200,30,0	0/0:50:0,50,200	0/0:40:0,40,200	1/1:30:200,30,0	0/0:50:0,50,200	1/1:30:200,30,0
-1	10250	.	A	C	99	PASS	TestDescription=HomVar/HomRef/HomVar	GT:GQ:PL	1/1:40:200,40,0	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	1/1:50:200,50,0	1/1:40:200,40,0
-1	10257	.	A	C	99	PASS	TestDescription=HomVar/Het/HomRef	GT:GQ:PL	1/1:50:200,50,0	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/0:30:0,30,200	1/1:50:200,50,0
-1	10285	.	T	C	99	PASS	TestDescription=HomVar/HomVar/Het	GT:GQ:PL	1/1:30:200,30,0	1/1:50:200,50,0	0/1:40:40,0,200	1/1:30:200,30,0	0/1:40:40,0,200	1/1:30:200,30,0
-1	10297	.	C	T	99	PASS	TestDescription=HomVar/HomVar/HomRef	GT:GQ:PL	1/1:40:200,40,0	1/1:30:200,30,0	0/0:50:0,50,200	1/1:40:200,40,0	0/0:50:0,50,200	1/1:40:200,40,0

public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.Special.vcf

@@ -1,20 +0,0 @@
-##fileformat=VCFv4.0
-##PhaseByTransmissionUnitTest="This file contains special cases for phasing by transmission such as missing genotypes. The unrelated individual should remain untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_FATHER	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
-1	10109	.	A	T	99	PASS	TestDescription=NoCall_mother	GT:GQ:PL	./.:.:.	0/0:40:0,40,200	0/1:30:30,0,200	./.:.:.	0/1:30:30,0,200	./.:.:.	
-1	10147	.	C	A	99	PASS	TestDescription=NoCall_father	GT:GQ:PL	0/0:30:0,30,200	./.:.:.	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200	
-1	10150	.	C	T	99	PASS	TestDescription=NoCall_child	GT:GQ:PL	0/0:40:0,40,200	0/1:30:30,0,200	./.:.:.	0/0:40:0,40,200	./.:.:.	0/0:40:0,40,200
-1	10177	.	A	C	99	PASS	TestDescription=Missing_mother	GT:GQ:PL	.	1/1:40:200,40,0	0/0:30:0,30,200	.	0/0:30:0,30,200	.
-1	10180	.	T	C	99	PASS	TestDescription=Missing_father	GT:GQ:PL	0/0:30:0,30,200	.	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200
-1	10234	.	C	T	99	PASS	TestDescription=Missing_child	GT:GQ:PL	0/1:40:40,0,200	0/0:30:0,30,200	.	0/1:40:40,0,200	.	0/1:40:40,0,200
-1	10235	.	T	A	99	PASS	TestDescription=NoCall_parents	GT:GQ:PL	./.:.:.	./.:.:.	0/0:30:0,30,200	./.:.:.	0/0:30:0,30,200	./.:.:.
-1	10236	.	A	G	99	PASS	TestDescription=NoCall_all	GT:GQ:PL	./.:.:.	./.:.:.	./.:.:.	./.:.:.	./.:.:.	./.:.:.
-1	10250	.	A	C	99	PASS	TestDescription=Missing_parents	GT:GQ:PL	.	.	1/1:50:200,50,0	.	1/1:50:200,50,0	.
-1	10257	.	A	C	99	PASS	TestDescription=Missing_all	GT:GQ:PL	.	.	.	.	.	.
-1	10285	.	T	C	99	PASS	TestDescription=ZeroConfidence	GT:GQ:PL	0/1:0:0,0,0	1/1:0:0,0,0	1/1:0:0,0,0	0/1:0:0,0,0	1/1:0:0,0,0	0/1:0:0,0,0
-1	10297	.	C	T	99	PASS	TestDescription=ZeroConfidenceParents	GT:GQ:PL	1/1:0:0,0,0	0/0:0:0,0,0	0/1:10:10,0,50	1/1:0:0,0,0	0/1:10:10,0,50	1/1:0:0,0,0
-1	10304	.	A	C	99	PASS	TestDescription=ZeroConfidenceChild	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:0:0,0,0	1/1:50:200,50,0	0/1:0:0,0,0	1/1:50:200,50,0

public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TN.vcf

@@ -1,22 +0,0 @@
-##fileformat=VCFv4.0
-##PhaseByTransmissionUnitTest="This file contains only genotypes of high quality and no mendelian violation in the input data. The output data should phase the trio and pair except for the Het/Het/Het case and leave the unrelated individual untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_FATHER	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
-1	10109	.	A	T	99	PASS	TestDescription=HomRef/HomRef/HomRef	GT:GQ:PL	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	
-1	10147	.	C	A	99	PASS	TestDescription=HomRef/Het/HomRef	GT:GQ:PL	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	0/0:50:0,50,200	
-1	10150	.	C	T	99	PASS	TestDescription=HomRef/Het/Het	GT:GQ:PL	0/0:50:0,50,200	0/1:50:50,0,200	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200
-1	10177	.	A	C	99	PASS	TestDescription=HomRef/HomAlt/Het	GT:GQ:PL	0/0:50:0,50,200	1/1:50:200,50,0	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200
-1	10180	.	T	C	99	PASS	TestDescription=Het/HomRef/HomRef	GT:GQ:PL	0/1:50:50,0,200	0/0:50:0,50,200	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200
-1	10234	.	C	T	99	PASS	TestDescription=Het/HomRef/Het	GT:GQ:PL	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200
-1	10235	.	T	A	99	PASS	TestDescription=Het/Het/HomRef	GT:GQ:PL	0/1:50:50,0,200	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200	0/0:50:0,50,200	0/1:50:50,0,200
-1	10236	.	A	G	99	PASS	TestDescription=Het/Het/Het	GT:GQ:PL	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200	0/1:50:50,0,200
-1	10250	.	A	C	99	PASS	TestDescription=Het/Het/HomVar	GT:GQ:PL	0/1:50:50,0,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:50,0,200
-1	10257	.	A	C	99	PASS	TestDescription=Het/HomVar/Het	GT:GQ:PL	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	0/1:50:50,0,200	0/1:50:200,0,50	0/1:50:50,0,200
-1	10285	.	T	C	99	PASS	TestDescription=Het/HomVar/HomVar	GT:GQ:PL	0/1:50:50,0,200	1/1:50:200,50,0	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:50,0,200
-1	10297	.	C	T	99	PASS	TestDescription=HomVar/HomRef/Het	GT:GQ:PL	1/1:50:200,50,0	0/0:50:0,50,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	1/1:50:200,50,0
-1	10304	.	A	C	99	PASS	TestDescription=HomVar/Het/Het	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	1/1:50:200,50,0
-1	10310	.	A	C	99	PASS	TestDescription=HomVar/Het/HomVar	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0
-1	10315	.	C	T	99	PASS	TestDescription=HomVar/HomVar/HomVar	GT:GQ:PL	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0

public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TP.vcf

@@ -1,19 +0,0 @@
-##fileformat=VCFv4.0
-##PhaseByTransmissionUnitTest="This file contains only genotypes of high quality true mendelian violations in the input data. The output data should not be able to phase the trios. The pair is phased where there is not enough information to distinguish a MV from a correct descent. Genotype combination phred score should be reported where possible. The unrelated individual should remain untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_FATHER	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
-1	10109	.	A	T	99	PASS	TestDescription=HomRef/HomRef/Het	GT:GQ:PL	0/0:80:0,80,200	0/0:80:0,80,200	0/1:80:80,0,200	0/0:80:0,80,200	0/1:80:80,0,200	0/0:80:0,80,200	
-1	10147	.	C	A	99	PASS	TestDescription=HomRef/HomRef/HomAlt	GT:GQ:PL	0/0:80:0,80,200	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	
-1	10150	.	C	T	99	PASS	TestDescription=HomRef/Het/HomAlt	GT:GQ:PL	0/0:80:0,80,200	0/1:80:80,0,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200
-1	10177	.	A	C	99	PASS	TestDescription=HomRef/HomAlt/HomRef	GT:GQ:PL	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	0/0:80:0,80,200	0/0:80:0,80,200	0/0:80:0,80,200
-1	10180	.	T	C	99	PASS	TestDescription=HomRef/HomAlt/HomAlt	GT:GQ:PL	0/0:80:0,80,200	1/1:80:200,80,0	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200
-1	10234	.	C	T	99	PASS	TestDescription=Het/HomRef/HomAlt	GT:GQ:PL	0/1:80:80,0,200	0/0:80:0,80,200	1/1:80:200,80,0	0/1:80:80,0,200	1/1:80:200,80,0	0/1:80:80,0,200
-1	10235	.	T	A	99	PASS	TestDescription=Het/HomAlt/HomRef	GT:GQ:PL	0/1:80:80,0,200	1/1:80:200,80,0	0/0:80:0,80,200	0/1:80:80,0,200	0/0:80:0,80,200	0/1:80:80,0,200
-1	10236	.	A	G	99	PASS	TestDescription=HomVar/HomRef/HomRef	GT:GQ:PL	1/1:80:200,80,0	0/0:80:0,80,200	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0
-1	10250	.	A	C	99	PASS	TestDescription=HomVar/HomRef/HomVar	GT:GQ:PL	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	1/1:80:200,80,0	1/1:80:200,80,0	1/1:80:200,80,0
-1	10257	.	A	C	99	PASS	TestDescription=HomVar/Het/HomRef	GT:GQ:PL	1/1:80:200,80,0	0/1:80:80,0,200	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0
-1	10285	.	T	C	99	PASS	TestDescription=HomVar/HomVar/Het	GT:GQ:PL	1/1:80:200,80,0	1/1:80:200,80,0	0/1:80:80,0,200	1/1:80:200,80,0	0/1:80:80,0,200	1/1:80:200,80,0
-1	10297	.	C	T	99	PASS	TestDescription=HomVar/HomVar/HomRef	GT:GQ:PL	1/1:80:200,80,0	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0	0/0:80:0,80,200	1/1:80:200,80,0

public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.goodFamilies.ped

@@ -1,6 +0,0 @@
-TRIO	TRIO_MOTHER	0	0	0	-9
-TRIO	TRIO_FATHER	0	0	1	-9
-TRIO	TRIO_CHILD	TRIO_FATHER	TRIO_MOTHER	0	-9
-PAIR	PAIR_FATHER	0	0	0	-9
-PAIR	PAIR_CHILD	PAIR_FATHER	0	1	-9
-UNRELATED	UNRELATED_INDIVIDUAL_CONTROL	0	0	0	-9

public/testdata/TabularDataTest.dat

@@ -1,7 +0,0 @@
-# comment
-# comment line
-#
-HEADER    COL1        COL2        COL3
-chrM:10     A       B       C
-chrM:20     C       D       E
-chrM:30     F       G       H

public/testdata/TabularDataTest2.dat

@@ -1,7 +0,0 @@
-# comment
-# comment line
-#
-HEADER,COL1,COL2,COL3,COL4
-chrM:10,A,B,C,1
-chrM:20,C,D,E,2
-chrM:30,F,G,H,3

public/testdata/VQSR.mixedTest.input

@@ -1,24 +0,0 @@
-##fileformat=VCFv4.1
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth">
-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
-##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
-##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
-##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
-##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-20	1000177	.	C	T	345	PASS	AC=43;AF=0.02053;AN=2094;BaseQRankSum=-0.234;DP=3748;DS;FS=5.678;HRun=2;HaplotypeScore=35.9850;InbreedingCoeff=0.0715;MQ=67.54;MQ0=0;MQRankSum=-0.549;QD=0.53;ReadPosRankSum=-13.245;set=EUR.admix
-20	1000177	.	CA	C	82.64	PASS	AC=43;AF=0.02053;AN=2094;BaseQRankSum=-0.234;DP=3748;DS;FS=5.678;HRun=2;HaplotypeScore=35.9850;InbreedingCoeff=0.0715;MQ=67.54;MQ0=0;MQRankSum=-0.549;QD=0.53;ReadPosRankSum=-13.245;set=EUR.admix
-20	1000382	.	C	G	456	PASS	AC=19;AF=0.00996;AN=1908;BaseQRankSum=3.153;DP=1249;FS=12.307;HRun=0;HaplotypeScore=25.9702;InbreedingCoeff=0.0716;MQ=49.54;MQ0=22;MQRankSum=-5.327;QD=2.71;ReadPosRankSum=-8.146;set=ASN.admix
-20	1000382	.	CCAAT	C	246.44	PASS	AC=19;AF=0.00996;AN=1908;BaseQRankSum=3.153;DP=1249;FS=12.307;HRun=0;HaplotypeScore=25.9702;InbreedingCoeff=0.0716;MQ=49.54;MQ0=22;MQRankSum=-5.327;QD=2.71;ReadPosRankSum=-8.146;set=ASN.admix
-20	1000442	rs112800484	TTTCA	T	28592.75	PASS	AC=1034;AF=0.69583;AN=1486;BaseQRankSum=19.864;DB;DP=1304;FS=31.497;HRun=0;HaplotypeScore=17.6398;InbreedingCoeff=0.2728;MQ=46.55;MQ0=85;MQRankSum=-6.417;QD=30.65;ReadPosRankSum=-2.058;set=EUR.admix

public/testdata/VQSR.mixedTest.recal

@@ -1,7 +0,0 @@
-##fileformat=VCFv4.1
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	
-20	1000177	.	N	<VQSR>	.	.	END=1000177;VQSLOD=-1.2345;culprit=FS
-20	1000177	.	N	<VQSR>	.	.	END=1000178;VQSLOD=-1.2377;culprit=HaplotypeScore
-20	1000382	.	N	<VQSR>	.	.	END=1000386;VQSLOD=-0.5534;culprit=HaplotypeScore
-20	1000382	.	N	<VQSR>	.	.	END=1000382;VQSLOD=-0.5678;culprit=FS
-20	1000442	.	N	<VQSR>	.	.	END=1000446;VQSLOD=3.5923;culprit=QD

public/testdata/VQSR.mixedTest.tranches

@@ -1,7 +0,0 @@
-# Variant quality score tranches file
-# Version number 4
-targetTruthSensitivity,numKnown,numNovel,knownTiTv,novelTiTv,minVQSLod,filterName,accessibleTruthSites,callsAtTruthSites,truthSensitivity
-90.00,17160,9743,0.0000,0.0000,2.3848,TruthSensitivityTranche0.00to90.00,9065,8158,0.8999
-99.00,21283,82814,0.0000,0.0000,-1.2413,TruthSensitivityTranche90.00to99.00,9065,8974,0.9900
-99.90,21845,92768,0.0000,0.0000,-6.9203,TruthSensitivityTranche99.00to99.90,9065,9055,0.9989
-100.00,21969,94464,0.0000,0.0000,-402.3663,TruthSensitivityTranche99.90to100.00,9065,9065,1.0000

public/testdata/ValidatingPileupTargets.list

@@ -1,29 +0,0 @@
-# e.coli
-/humgen/gsa-scr1/GATK_Data/Validation_Data/MV1994.bam         /humgen/gsa-scr1/GATK_Data/Validation_Data/Escherichia_coli_K12_MG1655.fasta      *
-
-# daughter chrom 6 deep coverage first 10 MB
-/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam  /broad/1KG/reference/human_b36_both.fasta   1:10,500,000-11,000,000
-
-# daughter chrom 1 deep coverage
-/broad/1KG/DCC/ftp/pilot_data/NA12878/alignment/NA12878.chrom1.SLX.SRP000032.2009_06.bam  /broad/1KG/reference/human_b36_both.fasta *
-
-# mother of trio individual low coverage
-/broad/1KG/DCC/ftp/pilot_data/NA12892/alignment/NA12892.SLX.SRP000031.2009_06.bam         /broad/1KG/reference/human_b36_both.fasta *
-
-# Pilot 3
-/broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *
-
-# anthony PCR lane
-# samtools import /seq/references/Homo_sapiens_assembly17/v0/Homo_sapiens_assembly17.bam.ref_list /seq/dirseq/aphilipp/combo/sequences/pcr/samfiles/10035.5.clean.sam 10035.5.clean.bam
-/humgen/gsa-scr1/GATK_Data/Validation_Data/10035.5.clean.bam /humgen/gsa-scr1/GATK_Data/Validation_Data/Homo_sapiens_assembly17.fasta *
-
-# anthony HS lane
-# samtools import /seq/references/Homo_sapiens_assembly17/v0/Homo_sapiens_assembly17.bam.ref_list /seq/dirseq/aphilipp/combo/sequences/hs/samfiles/30CLA.5.clean.sam 30CLA.5.clean.bam
-/humgen/gsa-scr1/GATK_Data/Validation_Data/30CLA.5.clean.bam /humgen/gsa-scr1/GATK_Data/Validation_Data/Homo_sapiens_assembly17.fasta *
-
-# whole exom interval-based analysis for cancer
-/humgen/gsa-scr1/GATK_Data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam         /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta      /humgen/gsa-scr1/GATK_Data/Validation_Data/TCGA-06-0188.interval_list
-
-# WGS tumor -- figure it out
-#/broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *
-

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.HG00625.vcf

@@ -1,25 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Validation_Data/VariantEval/FundamentalsTest.annotated.db.subset.final.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=[HG00625] select_expressions=[] excludeNonVariants=false excludeFiltered=false"
-##source=SelectVariants
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00625
-20	10003358	rs926982	A	C	92318.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=1	GT:DP:GQ:PL	1/1:1:3:27,3,0
-20	10003692	rs2064653	A	G	119873.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=3	GT:DP:GQ:PL	1/1:3:9:112,9,0
-20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.
-20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.
-20	10019093	rs575534	A	G	69795.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=5;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	1/1:5:15:172,15,0
-20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=2;DBSNP129;DBSNP132;DP=4;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,144
-20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=2;DBSNP132;DP=5;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,182
-20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=2;DBSNP129;DP=1;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	0/0:1:3:0,3,37
-20	10047435	rs598275	G	A	82495.04	PASS	AC=2;AF=1.00;AN=2;DBSNP129;DBSNP132;DP=4;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:4:12:139,12,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.NA12045.vcf

@@ -1,23 +0,0 @@
-##fileformat=VCFv4.1
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12045
-20	10003358	rs926982	A	C	92318.04	PASS	DBSNP129;DBSNP132;DP=5	GT:DP:GQ:PL	0/1:5:51:51,0,95
-20	10003692	rs2064653	A	G	119873.04	PASS	DBSNP129;DBSNP132;DP=4	GT:DP:GQ:PL	0/1:4:20:20,0,85
-20	10015679	rs113024248	C	.	2829.33	PASS	DBSNP132;DP=0;OMNI	GT:DP:PL	./.
-20	10015790	rs114356776	G	.	43.60	PASS	DBSNP132;DP=0	GT:DP:PL	./.
-20	10019093	rs575534	A	G	69795.04	PASS	DBSNP129;DBSNP132;DP=6;OMNI	GT:DP:GQ:PL	0/0:6:18:0,18,211
-20	10019169	rs7260784	C	.	1193.61	PASS	DBSNP129;DBSNP132;DP=6;HAPMAP;OMNI	GT:DP:GQ:PL	0/0:6:18:0,18,211
-20	10032432	rs78089752	A	.	367.04	PASS	DBSNP132;DP=8;OMNI	GT:DP:GQ:PL	0/0:8:24:0,24,293
-20	10037119	.	G	.	469.85	PASS	DBSNP129;DP=2	GT:DP:GQ:PL	0/0:2:6:0,6,65
-20	10047435	rs598275	G	A	82495.04	PASS	DBSNP129;DBSNP132;DP=2;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.split_1_of_2.vcf

@@ -1,19 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
-20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
-20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
-20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
-20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.split_2_of_2.vcf

@@ -1,18 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
-20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
-20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
-20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.final.vcf

@@ -1,23 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
-20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
-20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
-20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
-20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0
-20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
-20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
-20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
-20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/VariantEval/FundamentalsTest.annotated.db.subset.snps_and_indels.vcf

@@ -1,26 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	4680094	rs112637437	CCATGGTGGTGGCTGGGGACAGCCT	C	3590.76	PASS	NONCPG;AC=12;AF=0.0625;AN=192;DB;DP=1386;Dels=0.04;HRun=1;HaplotypeScore=3.9792;MQ=57.75;MQ0=6;QD=21.89;SB=-1275.83;sumGLbyD=21.89	GT:DP:GQ:PL	0/0:28:51.14:0,51,1539	0/1:8:99:287,0,160	0/1:10:99:549,0,338
-20	10003358	rs926982	A	C	92318.04	PASS	NONCPG;AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0
-20	10003692	rs2064653	A	G	119873.04	PASS	NONCPG;AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
-20	10015679	rs113024248	C	.	2829.33	PASS	CPG;AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
-20	10015790	rs114356776	G	.	43.60	FAIL	CPG;AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.
-20	10019093	rs575534	A	G	69795.04	PASS	NONCPG;AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=missense;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0
-20	10019169	rs7260784	C	.	1193.61	PASS	NONCPG;AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144
-20	10032432	rs78089752	A	.	367.04	PASS	NONCPG;AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182
-20	10037119	.	G	.	469.85	PASS	NONCPG;AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37
-20	10047435	rs598275	G	A	82495.04	FAIL	CPG;AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0
-20	31384616	.	A	AG	12610.94	PASS	NONCPG;AC=96;AF=0.5000;AN=192;DP=5288;Dels=0.00;HRun=2;HaplotypeScore=9.2447;MQ=61.14;MQ0=0;QD=2.38;SB=-2.03;sumGLbyD=2.39	GT:DP:GQ:PL	0/1:50:99:161,0,486	0/1:55:99:123,0,615	0/1:51:87.95:88,0,647
-20	62172300	.	CGG	C	440.96	FAIL	CPG;AC=25;AF=0.1316;AN=190;DP=2673;Dels=0.01;HRun=1;HaplotypeScore=12.2310;MQ=58.24;MQ0=0;QD=0.63;SB=-58.90;sumGLbyD=1.00	GT:DP:GQ:PL	0/0:29:45.69:0,46,1437	0/0:16:16.13:0,16,799	0/1:31:32.81:33,0,1141

public/testdata/VariantEval/MendelianViolationEval.ped

@@ -1,6 +0,0 @@
-TRIO	TRIO_MOTHER	0	0	0	-9
-TRIO	TRIO_FATHER	0	0	1	-9
-TRIO	TRIO_CHILD	TRIO_MOTHER	TRIO_FATHER	0	-9
-PAIR	PAIR_PARENT	0	0	0	-9
-PAIR	PAIR_CHILD	PAIR_PARENT	0	1	-9
-UNRELATED	UNRELATED_INDIVIDUAL_CONTROL	0	0	0	-9

public/testdata/VariantEval/MendelianViolationEval.vcf

@@ -1,22 +0,0 @@
-##fileformat=VCFv4.0
-##MendelianViolationEvaluator="This file contains genotypes with mendelian violations in the input data. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	TRIO_MOTHER	TRIO_FATHER	TRIO_CHILD	PAIR_PARENT	PAIR_CHILD	UNRELATED_INDIVIDUAL_CONTROL
-1	10109	.	A	T	99	PASS	.	GT:GQ:PL	0/0:50:0,50,200	0/0:40:0,40,200	0/1:30:30,0,200	0/0:50:0,50,200	0/1:30:30,0,200	0/0:50:0,50,200	
-1	10147	.	C	A	99	PASS	.	GT:GQ:PL	0/0:30:0,30,200	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200	
-1	10150	.	C	T	99	PASS	.	GT:GQ:PL	0/0:40:0,40,200	0/1:30:30,0,200	1/1:50:200,50,0	0/0:40:0,40,200	1/1:50:200,50,0	0/0:40:0,40,200
-1	10177	.	A	C	99	PASS	.	GT:GQ:PL	0/0:50:0,50,200	1/1:40:200,40,0	0/0:30:0,30,200	0/0:50:0,50,200	0/0:30:0,30,200	0/0:50:0,50,200
-1	10180	.	T	C	99	PASS	.	GT:GQ:PL	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	0/0:30:0,30,200	1/1:40:200,40,0	0/0:30:0,30,200
-1	10234	.	C	T	99	PASS	.	GT:GQ:PL	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/1:40:40,0,200	1/1:50:200,50,0	0/1:40:40,0,200
-1	10235	.	T	A	99	PASS	.	GT:GQ:PL	0/1:50:50,0,200	1/1:40:200,40,0	0/0:30:0,30,200	0/1:50:50,0,200	0/0:30:0,30,200	0/1:50:50,0,200
-1	10236	.	A	G	99	PASS	.	GT:GQ:PL	1/1:30:200,30,0	0/0:50:0,50,200	0/0:40:0,40,200	1/1:30:200,30,0	0/0:50:0,50,200	1/1:30:200,30,0
-1	10250	.	A	C	99	PASS	.	GT:GQ:PL	1/1:40:200,40,0	0/0:30:0,30,200	1/1:50:200,50,0	1/1:40:200,40,0	1/1:50:200,50,0	1/1:40:200,40,0
-1	10257	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:40:40,0,200	0/0:30:0,30,200	1/1:50:200,50,0	0/0:30:0,30,200	1/1:50:200,50,0
-1	10285	.	T	C	99	PASS	.	GT:GQ:PL	1/1:30:200,30,0	1/1:50:200,50,0	0/1:40:40,0,200	1/1:30:200,30,0	0/1:40:40,0,200	1/1:30:200,30,0
-1	10297	.	C	T	99	PASS	.	GT:GQ:PL	1/1:40:200,40,0	1/1:30:200,30,0	0/0:50:0,50,200	1/1:40:200,40,0	0/0:50:0,50,200	1/1:40:200,40,0
-1	10304	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:0:0,0,0	1/1:50:200,50,0	0/1:0:0,0,0	1/1:50:200,50,0
-1	10304	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	0/1:50:50,0,200	1/1:50:200,50,0	0/1:50:200,0,50	1/1:50:200,50,0
-1	10310	.	A	C	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	0/1:50:50,0,200	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0
-1	10315	.	C	T	99	PASS	.	GT:GQ:PL	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0	1/1:50:200,50,0

public/testdata/VariantEval/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.subset.vcf

@@ -1,243 +0,0 @@
-##fileformat=VCFv4.0
-##FILTER=<ID=ABFilter,Description="AB  0.75 && DP  40">
-##FILTER=<ID=DPFilter,Description="DP  120 || SB  -0.10">
-##FILTER=<ID=FDRtranche0.00to0.10,Description="FDR tranche level at qual 0.06">
-##FILTER=<ID=FDRtranche0.10to1.00,Description="FDR tranche level at qual 0.03">
-##FILTER=<ID=FDRtranche1.00to2.00,Description="FDR tranche level at qual 0.02">
-##FILTER=<ID=FDRtranche2.00to10.00+,Description="FDR tranche level at qual  0.06">
-##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 = 4 && ((MQ0 / (1.0 * DP))  0.1)">
-##FILTER=<ID=Indel,Description="Overlaps a user-input mask">
-##FILTER=<ID=LowQual,Description="Low quality">
-##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">
-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GL,Number=3,Type=Float,Description="Log-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FilterLiftedVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/tmp/0.069557317373441.sorted.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=FilterLiftedVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub"
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
-##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=OQ,Number=1,Type=Float,Description="The original variant quality score">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
-##LiftoverVariants="input_file=[] interval_merging=ALL read_buffer_size=null unsafe=null sample_metadata=[] read_filter=[] rodBind=[/home/radon01/kiran/scr1/projects/DataProcessingPaper/results/newForStacey/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] read_group_black_list=null log_to_file=null logging_level=INFO intervals=null BTI_merge_rule=UNION debug_mode=false downsample_to_fraction=null DBSNP=null num_threads=1 quiet_output_mode=false analysis_type=LiftoverVariants rodToIntervalTrackName=null help=false validation_strictness=SILENT downsample_to_coverage=null excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta useOriginalQualities=false phone_home=STANDARD downsampling_type=null out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub chain=/humgen/gsa-hpprojects/GATK/data/Liftover_Chain_Files/hg18ToHg19.broad.over.chain newSequenceDictionary=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.dict"
-##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[20:10000000-10100000] excludeIntervals=null reference_sequence=/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sample=null select_expressions=[] excludeNonVariants=false excludeFiltered=false"
-##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-23/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-24/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-5/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-9/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-6/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-19/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-25/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-4/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-14/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-22/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-2/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-3/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-7/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-16/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-1/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-17/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-8/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-10/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-18/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-20/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-11/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-15/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-21/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-12/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam, /humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/Q-2970@gsa2-1-temp-13/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam] read_buffer_size=null read_filter=[] intervals=[chrX] excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[dbsnp,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod, interval,Intervals,chrX] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod hapmap=null hapmap_chip=null out=null err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=10000 num_threads=1 interval_merging=ALL read_group_black_list=null genotype_model=JOINT_ESTIMATE base_model=EMPIRICAL heterozygosity=7.8E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null platform=null min_base_quality_score=20 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 cap_base_quality_by_mapping_quality=false"
-##VariantFiltration="analysis_type=VariantFiltration input_file=[] read_buffer_size=null read_filter=[] intervals=null excludeIntervals=[chrM, chrY] reference_sequence=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta rodBind=[variant,VCF,wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.vcf, mask,Bed,wgs.v9/HiSeq.WGS.cleaned.indels.10.mask] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null hapmap=null hapmap_chip=null out=wgs.v9/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf err=null outerr=null filterZeroMappingQualityReads=false downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null useOriginalQualities=false validation_strictness=SILENT unsafe=null max_reads_at_locus=2147483647 num_threads=1 interval_merging=ALL read_group_black_list=null filterExpression=[] filterName=[] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Indel NO_HEADER=false"
-##source=SelectVariants
-##source=VariantOptimizer
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	10000117	rs4816203	C	T	77.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=59.70;MQ0=0;OQ=867.45;QD=13.77;SB=-268.09	GT:AD:DP:GL:GQ	0/1:36,27:63:-109.01,-18.98,-129.63:99
-20	10000211	rs4813908	C	T	273.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=0;HaplotypeScore=1.32;MQ=59.66;MQ0=0;OQ=913.43;QD=16.61;SB=-383.86	GT:AD:DP:GL:GQ	0/1:28,27:53:-110.59,-15.96,-95.89:99
-20	10000439	rs4816204	T	G	489.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.06;MQ0=0;OQ=2354.98;QD=29.44;SB=-1083.04	GT:AD:DP:GL:GQ	1/1:0,80:77:-239.15,-23.21,-0.06:99
-20	10000598	rs6057087	T	A	659.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=48;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.58;MQ0=0;OQ=1772.11;QD=36.92;SB=-761.69	GT:AD:DP:GL:GQ	1/1:0,48:48:-180.81,-14.46,-0.01:99
-20	10000694	rs6057088	G	A	276.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=1.78;MQ=49.18;MQ0=0;OQ=1128.96;QD=14.11;SB=-510.63	GT:AD:DP:GL:GQ	0/1:46,34:80:-140.27,-24.09,-169.48:99
-20	10000758	rs6057089	T	A	243.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=91;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=54.23;MQ0=0;OQ=3541.99;QD=38.92;SB=-1671.36	GT:AD:DP:GL:GQ	1/1:0,91:91:-353.20,-27.40,-0.02:99
-20	10001019	rs6077626	T	G	401.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=48.70;MQ0=2;OQ=712.45;QD=10.33;SB=-352.52	GT:AD:DP:GL:GQ	0/1:40,29:65:-94.10,-19.57,-146.27:99
-20	10001298	rs1535165	T	A	637.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=54.34;MQ0=0;OQ=2708.88;QD=36.61;SB=-1143.40	GT:AD:DP:GL:GQ	1/1:0,73:73:-274.49,-21.99,-0.02:99
-20	10001474	rs1535166	C	T	608.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=43.97;MQ0=0;OQ=2678.14;QD=38.26;SB=-1011.68	GT:AD:DP:GL:GQ	1/1:0,70:69:-271.42,-20.79,-0.02:99
-20	10001617	rs2876191	C	A	279.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.00;HRun=0;HaplotypeScore=1.84;MQ=59.17;MQ0=0;OQ=1439.09;QD=14.25;SB=-481.71	GT:AD:DP:GL:GQ	0/1:52,49:101:-177.61,-30.42,-186.45:99
-20	10001628	rs1535167	G	A	101.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=2.95;MQ=59.36;MQ0=0;OQ=3780.26;QD=40.22;SB=-1550.04	GT:AD:DP:GL:GQ	1/1:0,93:93:-377.03,-30.13,-2.37:99
-20	10001661	rs1535168	T	C	621.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.09;MQ0=0;OQ=2787.58;QD=34.41;SB=-1177.74	GT:AD:DP:GL:GQ	1/1:0,81:79:-282.37,-23.79,-0.02:99
-20	10001670	rs1535169	T	G	512.38	PASS	AC=2;AF=1.00;AN=2;DB;DP=80;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.21;MQ0=0;OQ=2852.67;QD=35.22;SB=-1272.32	GT:AD:DP:GL:GQ	1/1:0,81:80:-288.87,-24.09,-0.02:99
-20	10002058	rs4404352	T	G	305.05	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=1.11;MQ=57.60;MQ0=0;OQ=2628.53;QD=34.14;SB=-934.22	GT:AD:DP:GL:GQ	1/1:1,76:75:-266.46,-22.59,-0.03:99
-20	10002099	rs4555427	C	T	2.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=5;HaplotypeScore=0.47;MQ=56.02;MQ0=0;OQ=1117.99;QD=17.47;SB=-498.13	GT:AD:DP:GL:GQ	0/1:27,37:61:-133.46,-18.38,-95.58:99
-20	10002138	rs4569544	C	G	481.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=55.30;MQ0=0;OQ=2204.77;QD=40.09;SB=-1043.64	GT:AD:DP:GL:GQ	1/1:0,55:51:-224.08,-15.37,-0.01:99
-20	10002142	rs4417777	G	C	579.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=55.21;MQ0=0;OQ=2117.84;QD=39.22;SB=-975.74	GT:AD:DP:GL:GQ	1/1:0,54:49:-215.38,-14.76,-0.01:99
-20	10002470	rs2327260	C	T	0	FDRtranche2.00to10.00+	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=11;HaplotypeScore=1.75;MQ=47.38;MQ0=0;OQ=2328.93;QD=34.25;SB=-1076.99	GT:AD:DP:GL:GQ	1/1:0,68:61:-236.50,-18.38,-0.02:99
-20	10002478	.	A	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=46;Dels=0.00;HRun=7;HaplotypeScore=9.60;MQ=53.59;MQ0=0;OQ=111.85;QD=2.00;SB=59.21	GT:AD:DP:GL:GQ	0/1:47,9:46:-28.33,-13.86,-140.18:99
-20	10002625	rs2144570	G	T	624.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.02;MQ0=0;OQ=2238.72;QD=36.11;SB=-983.67	GT:AD:DP:GL:GQ	1/1:0,62:61:-227.47,-18.37,-0.01:99
-20	10003021	rs6057090	C	T	599.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.01;MQ0=0;OQ=2357.20;QD=38.64;SB=-1005.68	GT:AD:DP:GL:GQ	1/1:0,61:60:-239.32,-18.08,-0.02:99
-20	10003358	rs926982	A	C	283.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.78;MQ0=0;OQ=1239.40;QD=14.58;SB=-411.81	GT:AD:DP:GL:GQ	0/1:43,42:84:-152.52,-25.30,-151.13:99
-20	10003651	rs926984	T	C	632.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=89;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.17;MQ0=0;OQ=3208.86;QD=35.65;SB=-1068.08	GT:AD:DP:GL:GQ	1/1:0,90:89:-324.50,-26.81,-0.03:99
-20	10003692	rs2064653	A	G	614.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.43;MQ0=0;OQ=2247.29;QD=34.05;SB=-940.96	GT:AD:DP:GL:GQ	1/1:0,66:65:-228.34,-19.58,-0.03:99
-20	10003832	rs6057091	G	A	453.48	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.79;MQ0=0;OQ=2581.24;QD=40.33;SB=-971.37	GT:AD:DP:GL:GQ	1/1:0,64:64:-261.72,-19.28,-0.01:99
-20	10004094	rs1988590	A	C	5.37	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.00;HRun=3;HaplotypeScore=0.16;MQ=53.93;MQ0=0;OQ=1571.64;QD=30.82;SB=-600.05	GT:AD:DP:GL:GQ	1/1:0,51:46:-160.77,-13.86,-0.02:99
-20	10004147	rs1988591	A	G	22.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=2;HaplotypeScore=0.77;MQ=56.98;MQ0=0;OQ=1621.26;QD=30.59;SB=-586.00	GT:AD:DP:GL:GQ	1/1:0,53:50:-165.75,-15.08,-0.04:99
-20	10004193	.	G	T	112	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=60.87;MQ0=0;OQ=817.22;QD=15.13;SB=-391.14	GT:AD:DP:GL:GQ	0/1:25,29:51:-100.37,-15.36,-82.85:99
-20	10004351	rs6057092	C	G	541.07	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.32;MQ0=0;OQ=2906.33;QD=42.74;SB=-1364.94	GT:AD:DP:GL:GQ	1/1:0,68:67:-294.24,-20.19,-0.02:99
-20	10004389	rs6057093	T	G	609.61	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.09;MQ0=0;OQ=2210.27;QD=35.65;SB=-884.11	GT:AD:DP:GL:GQ	1/1:0,62:62:-224.63,-18.68,-0.02:99
-20	10004610	rs2064654	A	C	2.26	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=10.08;MQ=58.45;MQ0=0;OQ=3199.99;QD=35.56;SB=-1545.20	GT:AD:DP:GL:GQ	1/1:1,89:88:-323.60,-26.50,-0.02:99
-20	10004725	rs10485737	A	G	457.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=55.27;MQ0=0;OQ=850.43;QD=13.08;SB=-367.17	GT:AD:DP:GL:GQ	0/1:35,30:65:-107.90,-19.58,-141.57:99
-20	10004874	rs725567	A	C	315.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.89;MQ=59.30;MQ0=0;OQ=2956.73;QD=35.20;SB=-1190.16	GT:AD:DP:GL:GQ	1/1:0,84:83:-299.28,-25.00,-0.02:99
-20	10004887	rs725566	A	G	256.51	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=2.16;MQ=59.44;MQ0=0;OQ=1129.32;QD=13.61;SB=-455.56	GT:AD:DP:GL:GQ	0/1:44,39:82:-140.92,-24.70,-171.36:99
-20	10005010	rs725565	C	T	706.03	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2824.42;QD=39.23;SB=-1089.38	GT:AD:DP:GL:GQ	1/1:0,72:71:-286.04,-21.39,-0.02:99
-20	10005427	rs6057094	C	T	587.79	PASS	AC=2;AF=1.00;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2155.03;QD=39.91;SB=-1081.37	GT:AD:DP:GL:GQ	1/1:0,54:54:-219.10,-16.26,-0.01:99
-20	10005499	rs6077631	A	G	634.39	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2607.55;QD=35.72;SB=-1078.12	GT:AD:DP:GL:GQ	1/1:0,73:73:-264.36,-21.99,-0.02:99
-20	10005587	rs6108375	A	G	498.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.74;MQ0=0;OQ=1061.48;QD=14.95;SB=-522.04	GT:AD:DP:GL:GQ	0/1:35,36:70:-130.52,-21.08,-138.09:99
-20	10005723	rs6108376	A	G	529.34	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2687.35;QD=31.62;SB=-1283.54	GT:AD:DP:GL:GQ	1/1:0,85:83:-272.38,-25.03,-0.06:99
-20	10006291	rs6118856	G	A	172.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=59.54;MQ0=0;OQ=908.18;QD=11.08;SB=-459.38	GT:AD:DP:GL:GQ	0/1:53,29:82:-118.80,-24.70,-191.13:99
-20	10006404	rs926985	A	C	490.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.46;MQ0=0;OQ=2586.62;QD=33.59;SB=-921.26	GT:AD:DP:GL:GQ	1/1:0,77:75:-262.28,-22.59,-0.03:99
-20	10006682	rs6057095	T	A	131.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.98;MQ=59.43;MQ0=0;OQ=2662.92;QD=36.48;SB=-986.49	GT:AD:DP:GL:GQ	1/1:0,72:71:-269.90,-21.39,-0.02:99
-20	10007150	rs11904989	G	C	276.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=0.32;MQ=59.70;MQ0=0;OQ=742.20;QD=11.78;SB=-296.80	GT:AD:DP:GL:GQ	0/1:38,25:60:-95.59,-18.09,-157.44:99
-20	10007175	rs2207850	C	T	90.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=1;HaplotypeScore=1.76;MQ=59.69;MQ0=0;OQ=1294.38;QD=21.22;SB=-604.18	GT:AD:DP:GL:GQ	0/1:22,39:58:-150.19,-17.47,-75.88:99
-20	10007352	rs1884399	C	T	614.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=2708.19;QD=39.25;SB=-1162.02	GT:AD:DP:GL:GQ	1/1:0,69:68:-274.43,-20.49,-0.02:99
-20	10007531	rs1884400	A	G	493.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2611.60;QD=36.78;SB=-843.33	GT:AD:DP:GL:GQ	1/1:0,71:71:-264.76,-21.38,-0.02:99
-20	10007980	rs2876192	A	C	668.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.73;MQ0=0;OQ=3022.49;QD=34.35;SB=-1434.18	GT:AD:DP:GL:GQ	1/1:0,88:87:-305.86,-26.20,-0.03:99
-20	10008221	rs2876193	T	C	510.25	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.18;MQ0=0;OQ=2840.34;QD=36.41;SB=-1397.57	GT:AD:DP:GL:GQ	1/1:0,78:78:-287.64,-23.49,-0.02:99
-20	10008458	rs6087107	T	G	157.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=68;Dels=0.00;HRun=0;HaplotypeScore=2.88;MQ=52.94;MQ0=0;OQ=2398.43;QD=33.78;SB=-1015.12	GT:AD:DP:GL:GQ	1/1:0,71:68:-243.45,-20.48,-0.02:99
-20	10008742	rs12479925	G	T	146.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=2.37;MQ=35.86;MQ0=1;OQ=685.54;QD=12.24;SB=-274.47	GT:AD:DP:GL:GQ	0/1:26,30:43:-84.79,-12.96,-61.80:99
-20	10008951	.	A	C	553.29	Indel	AC=1;AF=0.50;AN=2;DP=43;Dels=0.00;HRun=1;HaplotypeScore=16.13;MQ=51.15;MQ0=0;QD=11.77;SB=-184.92	GT:AD:DP:GL:GQ	0/1:23,24:43:-71.58,-12.97,-70.23:99
-20	10009227	rs12481420	A	G	523.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=57.92;MQ0=0;OQ=1201.44;QD=19.70;SB=-625.90	GT:AD:DP:GL:GQ	0/1:22,39:61:-141.80,-18.37,-90.52:99
-20	10009246	rs4574174	A	G	634.47	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=56.62;MQ0=0;OQ=2711.91;QD=35.68;SB=-1179.49	GT:AD:DP:GL:GQ	1/1:0,76:75:-274.80,-22.59,-0.02:99
-20	10009400	rs6057096	T	A	7.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=73;Dels=0.00;HRun=5;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2788.17;QD=38.19;SB=-1314.62	GT:AD:DP:GL:GQ	1/1:0,73:73:-282.42,-21.98,-0.01:99
-20	10009512	rs6039657	C	G	565.55	PASS	AC=2;AF=1.00;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.53;MQ0=0;OQ=3160.94;QD=41.59;SB=-1228.86	GT:AD:DP:GL:GQ	1/1:0,76:74:-319.70,-22.30,-0.02:99
-20	10009719	rs6057097	A	G	58.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=1.82;MQ=59.33;MQ0=0;OQ=1551.35;QD=25.02;SB=-585.82	GT:AD:DP:GL:GQ	1/1:0,62:50:-158.78,-15.09,-0.06:99
-20	10009795	rs6118861	A	G	501.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.59;MQ0=0;OQ=1594.00;QD=35.42;SB=-578.40	GT:AD:DP:GL:GQ	1/1:0,45:45:-163.00,-13.55,-0.01:99
-20	10009844	rs6057098	G	A	11.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=1;HaplotypeScore=2.92;MQ=52.80;MQ0=0;OQ=1658.97;QD=30.16;SB=-750.39	GT:AD:DP:GL:GQ	0/1:8,47:51:-184.54,-15.37,-17.54:21.74
-20	10009871	rs6133780	A	G	1067.52	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=1;HaplotypeScore=16.85;MQ=51.54;MQ0=0;QD=18.09;SB=-387.29	GT:AD:DP:GL:GQ	0/1:19,40:49:-124.80,-14.77,-52.03:99
-20	10009875	rs6133781	A	G	1106.95	SnpCluster	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=1;HaplotypeScore=19.06;MQ=51.21;MQ0=0;QD=19.42;SB=-410.34	GT:AD:DP:GL:GQ	0/1:16,41:44:-127.23,-13.25,-35.68:99
-20	10009879	.	A	G	1218.05	SnpCluster	AC=2;AF=1.00;AN=2;DP=42;Dels=0.00;HRun=1;HaplotypeScore=20.77;MQ=51.40;MQ0=0;QD=23.88;SB=-543.65	GT:AD:DP:GL:GQ	1/1:5,46:42:-136.91,-12.65,-11.59:10.59
-20	10009883	rs6133782	A	G	1399.75	SnpCluster	AC=2;AF=1.00;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=11.88;MQ=52.16;MQ0=0;QD=27.45;SB=-484.45	GT:AD:DP:GL:GQ	1/1:2,49:43:-147.73,-12.95,-4.17:87.80
-20	10010393	rs513998	T	G	602.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.40;MQ0=0;OQ=1247.20;QD=16.20;SB=-518.70	GT:AD:DP:GL:GQ	0/1:35,42:76:-150.89,-22.89,-128.62:99
-20	10010766	rs517531	T	G	421.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=2100.93;QD=31.36;SB=-978.12	GT:AD:DP:GL:GQ	1/1:0,66:67:-217.39,-23.46,-3.72:99
-20	10010832	rs582827	T	C	733.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.50;MQ0=0;OQ=2668.46;QD=35.58;SB=-1048.08	GT:AD:DP:GL:GQ	1/1:0,75:75:-270.45,-22.59,-0.02:99
-20	10011075	rs6039659	C	T	234.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=1;HaplotypeScore=2.42;MQ=60.00;MQ0=0;OQ=1322.11;QD=15.74;SB=-644.72	GT:AD:DP:GL:GQ	0/1:45,39:82:-160.20,-24.71,-141.60:99
-20	10011309	rs641722	T	C	546.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=2396.22;QD=30.72;SB=-1026.41	GT:AD:DP:GL:GQ	1/1:0,78:76:-243.28,-22.92,-0.07:99
-20	10011666	rs546821	C	T	285.21	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2849.79;QD=40.14;SB=-1187.35	GT:AD:DP:GL:GQ	1/1:0,71:71:-288.58,-21.39,-0.02:99
-20	10011939	rs548863	C	T	181.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.09;MQ=56.14;MQ0=0;OQ=2488.04;QD=39.49;SB=-885.19	GT:AD:DP:GL:GQ	1/1:0,63:62:-252.40,-18.68,-0.01:99
-20	10012362	rs574425	G	T	17.09	PASS	AC=2;AF=1.00;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=51.41;MQ0=0;OQ=676.99;QD=28.21;SB=-89.90	GT:AD:DP:GL:GQ	1/1:0,24:20:-71.29,-6.02,-0.01:60.18
-20	10012384	rs7270107	T	C	128.88	PASS	AC=1;AF=0.50;AN=2;DB;DP=16;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=51.62;MQ0=0;OQ=216.13;QD=12.01;SB=-75.35	GT:AD:DP:GL:GQ	0/1:9,9:16:-29.72,-4.82,-34.04:99
-20	10012387	rs6057102	T	C	18.19	PASS	AC=2;AF=1.00;AN=2;DB;DP=11;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=50.47;MQ0=0;OQ=295.02;QD=18.44;SB=-77.36	GT:AD:DP:GL:GQ	1/1:0,16:11:-33.10,-3.32,-0.02:33.06
-20	10012479	rs575394	A	G	3.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=16;Dels=0.00;HRun=1;HaplotypeScore=1.18;MQ=49.52;MQ0=0;OQ=474.16;QD=23.71;SB=-247.57	GT:AD:DP:GL:GQ	1/1:0,20:16:-51.02,-4.83,-0.02:48.10
-20	10012498	rs657453	C	G	2.83	PASS	AC=2;AF=1.00;AN=2;DB;DP=9;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=40.06;MQ0=0;OQ=331.25;QD=22.08;SB=-84.82	GT:AD:DP:GL:GQ	1/1:0,15:9:-36.71,-2.71,-0.01:27.09
-20	10012518	rs657490	T	C	1.50	PASS	AC=2;AF=1.00;AN=2;DB;DP=12;Dels=0.00;HRun=1;HaplotypeScore=1.64;MQ=34.32;MQ0=0;OQ=366.95;QD=22.93;SB=-197.06	GT:AD:DP:GL:GQ	1/1:0,16:12:-40.29,-3.62,-0.01:36.09
-20	10012521	rs6141099	C	T	33.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=14;Dels=0.00;HRun=0;HaplotypeScore=1.64;MQ=35.97;MQ0=0;OQ=104.02;QD=5.78;SB=-64.27	GT:AD:DP:GL:GQ	0/1:11,7:14:-17.91,-4.23,-28.63:99
-20	10012636	rs57357029	G	C	442.35	Indel	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=3;HaplotypeScore=2.47;MQ=46.22;MQ0=1;QD=17.69;SB=-127.71	GT:AD:DP:GL:GQ	0/1:10,15:20:-53.56,-6.04,-26.16:99
-20	10012714	rs577258	G	C	4.14	PASS	AC=2;AF=1.00;AN=2;DB;DP=34;Dels=0.00;HRun=1;HaplotypeScore=0.97;MQ=54.18;MQ0=0;OQ=1374.69;QD=38.19;SB=-268.50	GT:AD:DP:GL:GQ	1/1:0,36:34:-141.07,-10.25,-0.02:99
-20	10012751	rs577383	T	C	3.88	PASS	AC=2;AF=1.00;AN=2;DB;DP=26;Dels=0.00;HRun=1;HaplotypeScore=2.10;MQ=51.17;MQ0=0;OQ=807.71;QD=26.06;SB=-389.47	GT:AD:DP:GL:GQ	1/1:0,31:26:-84.38,-7.84,-0.03:78.14
-20	10013119	rs670350	C	T	14.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=7.14;MQ=53.67;MQ0=0;OQ=1037.37;QD=17.58;SB=-503.12	GT:AD:DP:GL:GQ	0/1:27,32:57:-124.19,-17.17,-93.21:99
-20	10013574	rs6057108	G	A	190.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=1;HaplotypeScore=1.31;MQ=59.43;MQ0=0;OQ=995.08;QD=15.08;SB=-284.14	GT:AD:DP:GL:GQ	0/1:36,30:66:-122.67,-19.88,-129.26:99
-20	10015679	.	C	T	4.66	PASS	AC=1;AF=0.50;AN=2;DP=10;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=60.00;MQ0=0;OQ=130.84;QD=11.89;SB=-10.00	GT:AD:DP:GL:GQ	0/1:5,6:10:-19.38,-3.01,-17.14:99
-20	10015761	rs12106014	T	C	188.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.95;MQ0=0;OQ=282.39;QD=12.84;SB=-35.94	GT:AD:DP:GL:GQ	0/1:9,13:21:-37.85,-6.33,-34.21:99
-20	10018158	rs512313	G	C	152.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=1;HaplotypeScore=0.79;MQ=59.79;MQ0=0;OQ=1786.48;QD=20.53;SB=-749.98	GT:AD:DP:GL:GQ	0/1:39,47:85:-207.56,-25.63,-151.93:99
-20	10018555	rs570855	G	A	501.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1507.16;QD=18.61;SB=-748.62	GT:AD:DP:GL:GQ	0/1:36,45:80:-178.09,-24.09,-134.36:99
-20	10019093	rs575534	A	G	198.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=2;HaplotypeScore=1.33;MQ=59.34;MQ0=0;OQ=1097.34;QD=15.68;SB=-511.28	GT:AD:DP:GL:GQ	0/1:34,36:69:-133.80,-20.78,-132.32:99
-20	10020229	rs596203	G	A	334.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=1.85;MQ=59.76;MQ0=0;OQ=1448.48;QD=18.34;SB=-632.66	GT:AD:DP:GL:GQ	0/1:37,42:79:-171.94,-23.81,-120.12:99
-20	10023689	rs4813909	G	A	153.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.95;MQ=59.04;MQ0=0;OQ=1887.80;QD=22.74;SB=-948.03	GT:AD:DP:GL:GQ	0/1:30,53:83:-217.06,-25.00,-110.51:99
-20	10024107	.	C	T	114.08	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.93;MQ=59.56;MQ0=0;OQ=1618.74;QD=19.04;SB=-735.06	GT:AD:DP:GL:GQ	0/1:38,47:84:-190.47,-25.31,-121.49:99
-20	10024288	.	C	T	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=5;HaplotypeScore=7.93;MQ=51.94;MQ0=0;OQ=68.97;QD=0.97;SB=86.23	GT:AD:DP:GL:GQ	0/1:53,18:57:-27.36,-17.18,-167.04:99
-20	10024294	.	C	T	19.74	DPFilter;LowQual	AC=1;AF=0.50;AN=2;DP=51;Dels=0.00;HRun=5;HaplotypeScore=23.45;MQ=49.01;MQ0=1;QD=0.27;SB=83.26	GT:AD:DP:GL:GQ	0/1:55,18:51:-20.62,-15.37,-156.17:52.53
-20	10026357	rs685723	T	C	589.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=58.91;MQ0=0;OQ=1010.93;QD=16.57;SB=-474.08	GT:AD:DP:GL:GQ	0/1:26,35:60:-122.45,-18.07,-104.85:99
-20	10026794	rs687514	C	T	152.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=1.87;MQ=60.00;MQ0=0;OQ=1015.27;QD=19.52;SB=-447.00	GT:AD:DP:GL:GQ	0/1:19,32:49:-119.58,-14.77,-61.54:99
-20	10027868	rs514832	A	G	410.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.82;MQ=59.47;MQ0=0;OQ=1149.09;QD=13.21;SB=-556.55	GT:AD:DP:GL:GQ	0/1:43,44:87:-144.42,-26.22,-173.75:99
-20	10027872	rs594811	A	G	112.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=2;HaplotypeScore=0.67;MQ=59.44;MQ0=0;OQ=1351.31;QD=16.28;SB=-565.56	GT:AD:DP:GL:GQ	0/1:39,44:83:-163.41,-25.00,-161.96:99
-20	10030188	rs652633	T	A	473.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.71;MQ0=0;OQ=1186.53;QD=15.02;SB=-453.42	GT:AD:DP:GL:GQ	0/1:41,38:79:-145.73,-23.79,-157.38:99
-20	10031342	rs668091	G	A	109.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=2;HaplotypeScore=1.52;MQ=60.00;MQ0=0;OQ=1739.31;QD=19.11;SB=-748.28	GT:AD:DP:GL:GQ	0/1:41,50:90:-204.32,-27.11,-145.56:99
-20	10031798	rs669985	G	A	353.33	PASS	AC=2;AF=1.00;AN=2;DB;DP=104;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.60;MQ0=0;OQ=4247.21;QD=40.84;SB=-1915.55	GT:AD:DP:GL:GQ	1/1:0,104:104:-423.72,-31.33,-0.03:99
-20	10031827	rs558493	C	T	27.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=108;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.83;MQ0=0;OQ=1957.26;QD=18.12;SB=-1004.58	GT:AD:DP:GL:GQ	0/1:52,56:108:-231.54,-32.53,-189.42:99
-20	10032094	rs681750	G	A	562.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.21;QD=14.16;SB=-575.44	GT:AD:DP:GL:GQ	0/1:47,36:82:-145.51,-24.71,-151.92:99
-20	10032413	rs683145	T	G	535.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=698.84;QD=11.09;SB=-317.98	GT:AD:DP:GL:GQ	0/1:33,30:63:-92.15,-18.98,-124.49:99
-20	10032882	rs479039	A	T	24.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.01;HRun=0;HaplotypeScore=7.14;MQ=58.99;MQ0=0;OQ=1029.41;QD=13.73;SB=-439.55	GT:AD:DP:GL:GQ	0/1:40,34:73:-128.21,-21.99,-155.80:99
-20	10034306	rs604452	T	C	170.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.92;MQ=59.46;MQ0=0;OQ=667.43;QD=8.67;SB=-359.16	GT:AD:DP:GL:GQ	0/1:47,29:73:-92.02,-22.00,-181.63:99
-20	10037037	rs2327261	C	T	271.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.97;MQ0=0;OQ=1384.69;QD=17.53;SB=-468.51	GT:AD:DP:GL:GQ	0/1:38,41:74:-164.05,-22.30,-111.89:99
-20	10037709	rs518364	A	T	403.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=1.49;MQ=59.68;MQ0=0;OQ=896.68;QD=12.63;SB=-381.55	GT:AD:DP:GL:GQ	0/1:39,32:70:-114.04,-21.09,-148.36:99
-20	10039371	rs678696	T	G	586.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1105.57;QD=15.79;SB=-406.66	GT:AD:DP:GL:GQ	0/1:32,38:70:-134.92,-21.08,-120.34:99
-20	10040821	rs6057119	T	A	1156.74	Indel	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.03;HRun=6;HaplotypeScore=36.61;MQ=50.69;MQ0=0;QD=15.22;SB=-511.29	GT:AD:DP:GL:GQ	0/1:35,39:75:-140.95,-21.99,-129.69:99
-20	10041304	rs559129	C	T	83.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.92;MQ=59.66;MQ0=0;OQ=2692.91;QD=39.60;SB=-1319.36	GT:AD:DP:GL:GQ	1/1:0,68:67:-272.89,-20.18,-0.01:99
-20	10042319	rs631317	C	T	711.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.00;MQ0=0;OQ=2553.65;QD=39.29;SB=-1137.05	GT:AD:DP:GL:GQ	1/1:0,65:64:-258.97,-19.28,-0.02:99
-20	10042761	rs633445	A	G	631.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=88;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=3233.06;QD=35.53;SB=-1142.81	GT:AD:DP:GL:GQ	1/1:0,91:88:-327.18,-26.51,-0.02:99
-20	10042829	rs633841	A	G	305.65	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.76;MQ0=0;OQ=2746.23;QD=35.21;SB=-1237.83	GT:AD:DP:GL:GQ	1/1:0,78:77:-278.24,-23.20,-0.03:99
-20	10043002	.	A	T	147.57	PASS	AC=1;AF=0.50;AN=2;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1103.68;QD=13.14;SB=-535.28	GT:AD:DP:GL:GQ	0/1:48,36:84:-138.95,-25.30,-175.62:99
-20	10044849	rs663380	A	G	242.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=60.00;MQ0=0;OQ=1840.58;QD=31.20;SB=-654.96	GT:AD:DP:GL:GQ	1/1:0,59:57:-187.68,-17.18,-0.04:99
-20	10045078	rs674630	G	T	86.82	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.00;HRun=2;HaplotypeScore=1.98;MQ=58.99;MQ0=0;OQ=2874.89;QD=36.39;SB=-1368.13	GT:AD:DP:GL:GQ	1/1:0,79:78:-291.09,-23.49,-0.02:99
-20	10045642	rs572752	G	C	658.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.77;MQ0=0;OQ=3374.18;QD=42.18;SB=-1455.16	GT:AD:DP:GL:GQ	1/1:0,80:79:-336.42,-23.81,-0.03:99
-20	10046537	rs583827	A	G	86.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=55;Dels=0.00;HRun=0;HaplotypeScore=5.76;MQ=54.17;MQ0=0;OQ=719.43;QD=12.40;SB=-246.31	GT:AD:DP:GL:GQ	0/1:29,29:55:-91.80,-16.57,-108.67:99
-20	10050828	rs660454	T	C	314.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.94;MQ=59.73;MQ0=0;OQ=1072.85;QD=12.62;SB=-513.86	GT:AD:DP:GL:GQ	0/1:48,37:84:-135.87,-25.30,-193.36:99
-20	10051448	rs565455	T	C	358.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=2.24;MQ=59.41;MQ0=0;OQ=1005.69;QD=14.16;SB=-400.33	GT:AD:DP:GL:GQ	0/1:36,35:69:-124.64,-20.79,-133.98:99
-20	10052688	.	C	A	247.91	PASS	AC=1;AF=0.50;AN=2;DP=77;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.76;MQ0=0;OQ=928.77;QD=12.06;SB=-460.78	GT:AD:DP:GL:GQ	0/1:45,32:77:-119.35,-23.19,-165.26:99
-20	10058022	rs531797	T	C	82.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=6.22;MQ=58.46;MQ0=0;OQ=872.91;QD=12.47;SB=-339.92	GT:AD:DP:GL:GQ	0/1:38,32:67:-110.76,-20.18,-144.54:99
-20	10067090	rs507568	C	A	124.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=50;Dels=0.00;HRun=0;HaplotypeScore=-0.12;MQ=55.67;MQ0=0;OQ=1789.54;QD=33.76;SB=-802.84	GT:AD:DP:GL:GQ	1/1:0,53:50:-182.55,-15.06,-0.02:99
-20	10067264	rs530271	G	A	217.29	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.68;MQ0=0;OQ=2865.42;QD=39.80;SB=-1324.28	GT:AD:DP:GL:GQ	1/1:0,72:72:-290.15,-21.69,-0.02:99
-20	10067722	rs604416	A	C	278.06	PASS	AC=2;AF=1.00;AN=2;DB;DP=52;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1822.34;QD=35.05;SB=-862.09	GT:AD:DP:GL:GQ	1/1:0,52:52:-185.83,-15.66,-0.02:99
-20	10068981	rs490505	G	A	49.73	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=1.07;MQ=59.55;MQ0=0;OQ=2469.03;QD=39.82;SB=-1135.04	GT:AD:DP:GL:GQ	1/1:0,62:61:-250.50,-18.37,-0.01:99
-20	10070602	rs6039684	T	C	187.72	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.72;MQ=58.71;MQ0=0;OQ=2364.76;QD=32.84;SB=-1139.10	GT:AD:DP:GL:GQ	1/1:0,72:69:-240.09,-20.79,-0.03:99
-20	10070936	.	T	A	3050.87	Indel	AC=2;AF=1.00;AN=2;DP=80;Dels=0.00;HRun=1;HaplotypeScore=2.65;MQ=58.76;MQ0=0;QD=37.67;SB=-1399.42	GT:AD:DP:GL:GQ	1/1:0,81:80:-308.69,-24.09,-0.02:99
-20	10071135	rs552048	C	T	173.64	PASS	AC=2;AF=1.00;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=0.47;MQ=59.09;MQ0=0;OQ=3089.23;QD=40.65;SB=-1301.70	GT:AD:DP:GL:GQ	1/1:0,76:76:-312.53,-22.89,-0.02:99
-20	10071187	rs6032780	G	A	696.17	PASS	AC=2;AF=1.00;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.72;MQ0=0;OQ=3367.02;QD=40.57;SB=-1247.04	GT:AD:DP:GL:GQ	1/1:0,83:82:-335.70,-24.70,-0.02:99
-20	10071890	rs6039685	T	C	547.16	PASS	AC=2;AF=1.00;AN=2;DB;DP=56;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.67;MQ0=0;OQ=1748.72;QD=30.68;SB=-861.55	GT:AD:DP:GL:GQ	1/1:0,57:56:-178.51,-16.89,-0.05:99
-20	10072505	rs6032786	A	G	465.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=57;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1789.94;QD=28.41;SB=-916.44	GT:AD:DP:GL:GQ	1/1:0,63:57:-182.63,-17.19,-0.05:99
-20	10074187	.	A	G	68.82	PASS	AC=2;AF=1.00;AN=2;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.70;MQ0=0;OQ=2702.25;QD=35.09;SB=-1331.57	GT:AD:DP:GL:GQ	1/1:0,77:77:-273.84,-23.20,-0.03:99
-20	10074240	rs614270	T	C	574.99	PASS	AC=2;AF=1.00;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.78;MQ0=0;OQ=2989.29;QD=34.76;SB=-1439.46	GT:AD:DP:GL:GQ	1/1:0,85:83:-302.53,-25.00,-0.02:99
-20	10074716	rs2327236	G	A	207.80	PASS	AC=2;AF=1.00;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=1.12;MQ=60.00;MQ0=0;OQ=2351.97;QD=35.10;SB=-934.35	GT:AD:DP:GL:GQ	1/1:0,67:62:-238.81,-18.69,-0.03:99
-20	10074806	rs2327237	G	A	618.46	PASS	AC=2;AF=1.00;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.68;MQ0=0;OQ=2806.22;QD=38.98;SB=-1369.05	GT:AD:DP:GL:GQ	1/1:0,72:71:-284.22,-21.39,-0.02:99
-20	10075043	rs617891	T	C	295.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=61;Dels=0.00;HRun=2;HaplotypeScore=0.00;MQ=59.62;MQ0=0;OQ=2170.63;QD=35.58;SB=-943.96	GT:AD:DP:GL:GQ	1/1:0,61:61:-220.67,-18.37,-0.02:99
-20	10075168	rs6032787	C	T	590.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=86;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.48;MQ0=0;OQ=3524.41;QD=40.05;SB=-1505.51	GT:AD:DP:GL:GQ	1/1:0,88:86:-351.44,-25.90,-0.02:99
-20	10076250	rs644043	A	G	293.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=59.71;MQ0=0;OQ=915.84;QD=11.59;SB=-456.82	GT:AD:DP:GL:GQ	0/1:41,38:77:-118.08,-23.21,-160.58:99
-20	10076339	rs644160	A	G	242.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=2.63;MQ=59.35;MQ0=0;OQ=1102.11;QD=15.52;SB=-557.03	GT:AD:DP:GL:GQ	0/1:33,38:71:-134.88,-21.39,-128.30:99
-20	10076399	rs506458	G	A	360.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=94;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1756.48;QD=18.69;SB=-796.27	GT:AD:DP:GL:GQ	0/1:44,50:94:-207.24,-28.31,-163.43:99
-20	10077752	.	T	C	195.33	PASS	AC=1;AF=0.50;AN=2;DP=79;Dels=0.00;HRun=0;HaplotypeScore=0.79;MQ=60.00;MQ0=0;OQ=1175.95;QD=14.89;SB=-463.61	GT:AD:DP:GL:GQ	0/1:34,45:79:-144.69,-23.81,-137.94:99
-20	10081750	rs473369	C	A	178.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=3;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1188.67;QD=14.50;SB=-583.96	GT:AD:DP:GL:GQ	0/1:43,39:82:-146.85,-24.69,-154.74:99
-20	10081800	rs474169	C	T	600.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1088.62;QD=16.25;SB=-544.01	GT:AD:DP:GL:GQ	0/1:34,33:67:-132.33,-20.18,-122.19:99
-20	10082892	rs644145	C	T	208.97	PASS	AC=2;AF=1.00;AN=2;DB;DP=41;Dels=0.00;HRun=0;HaplotypeScore=1.03;MQ=60.00;MQ0=0;OQ=1601.32;QD=38.13;SB=-762.50	GT:AD:DP:GL:GQ	1/1:0,42:41:-163.73,-12.35,-0.01:99
-20	10085211	rs685573	A	T	447.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.51;MQ0=0;OQ=1024.78;QD=13.48;SB=-509.23	GT:AD:DP:GL:GQ	0/1:42,34:75:-128.35,-22.59,-157.06:99
-20	10086110	rs592026	G	A	451.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.14;MQ0=0;OQ=1254.60;QD=15.49;SB=-639.16	GT:AD:DP:GL:GQ	0/1:43,38:81:-153.14,-24.40,-157.02:99
-20	10086283	rs592889	G	T	230.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=1.00;MQ=60.00;MQ0=0;OQ=882.77;QD=10.51;SB=-462.82	GT:AD:DP:GL:GQ	0/1:52,32:84:-116.86,-25.30,-180.39:99
-20	10086619	rs513535	T	A	1.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=5;HaplotypeScore=1.00;MQ=59.68;MQ0=0;OQ=746.98;QD=10.52;SB=-282.61	GT:AD:DP:GL:GQ	0/1:45,26:69:-98.76,-20.78,-164.07:99
-20	10086853	rs127733	G	A	343.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.92;MQ=59.75;MQ0=0;OQ=945.98;QD=12.78;SB=-472.45	GT:AD:DP:GL:GQ	0/1:42,32:71:-119.28,-21.40,-133.60:99
-20	10086954	rs595987	G	A	578.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1076.10;QD=16.06;SB=-401.89	GT:AD:DP:GL:GQ	0/1:33,34:66:-130.79,-19.89,-110.09:99
-20	10087230	rs607331	A	G	497.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=95;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.87;MQ0=0;OQ=1624.42;QD=17.10;SB=-744.63	GT:AD:DP:GL:GQ	0/1:41,54:95:-194.34,-28.62,-167.75:99
-20	10087394	rs608188	T	G	410.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=59.72;MQ0=0;OQ=1428.70;QD=17.21;SB=-695.70	GT:AD:DP:GL:GQ	0/1:35,48:83:-171.15,-25.00,-131.95:99
-20	10087754	rs544718	T	G	209.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.00;HRun=2;HaplotypeScore=0.92;MQ=60.45;MQ0=0;OQ=1195.66;QD=15.33;SB=-504.83	GT:AD:DP:GL:GQ	0/1:36,42:77:-146.04,-23.19,-131.14:99
-20	10087804	rs609932	C	T	337.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.00;HRun=0;HaplotypeScore=1.58;MQ=60.49;MQ0=0;OQ=1534.51;QD=15.35;SB=-666.41	GT:AD:DP:GL:GQ	0/1:50,50:93:-184.76,-28.03,-153.45:99
-20	10088063	rs621673	C	T	498.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.79;MQ0=0;OQ=1322.79;QD=15.20;SB=-531.00	GT:AD:DP:GL:GQ	0/1:46,41:84:-160.88,-25.32,-143.12:99
-20	10088699	rs498420	C	T	139.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.00;HRun=0;HaplotypeScore=3.78;MQ=54.80;MQ0=0;OQ=803.84;QD=12.18;SB=-217.49	GT:AD:DP:GL:GQ	0/1:38,28:61:-102.06,-18.39,-112.29:99
-20	10088730	rs624398	G	A	180.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.00;HRun=0;HaplotypeScore=2.57;MQ=52.02;MQ0=0;OQ=706.21;QD=12.39;SB=-215.65	GT:AD:DP:GL:GQ	0/1:29,26:51:-89.27,-15.37,-99.20:99
-20	10088736	rs624401	A	C	166.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.00;HRun=1;HaplotypeScore=2.26;MQ=51.41;MQ0=0;OQ=755.82;QD=12.81;SB=-289.77	GT:AD:DP:GL:GQ	0/1:29,29:53:-94.83,-15.97,-94.03:99
-20	10088747	rs624419	A	G	458.31	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=51.80;MQ0=0;OQ=732.27;QD=13.31;SB=-319.26	GT:AD:DP:GL:GQ	0/1:25,30:54:-92.79,-16.28,-99.03:99
-20	10088799	rs624824	G	A	1.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=8.99;MQ=54.24;MQ0=0;OQ=1015.57;QD=18.46;SB=-384.14	GT:AD:DP:GL:GQ	0/1:24,31:54:-121.12,-16.28,-76.29:99
-20	10088895	rs500269	C	T	289	PASS	AC=1;AF=0.50;AN=2;DB;DP=39;Dels=0.00;HRun=0;HaplotypeScore=0.83;MQ=58.39;MQ0=0;OQ=522.39;QD=12.74;SB=-237.72	GT:AD:DP:GL:GQ	0/1:24,17:39:-67.28,-11.76,-70.34:99
-20	10088985	rs2876185	T	C	0	FDRtranche2.00to10.00+	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=28.26;MQ=49.95;MQ0=0;OQ=805.93;QD=10.20;SB=-330.82	GT:AD:DP:GL:GQ	0/1:43,35:73:-105.88,-22.00,-156.93:99
-20	10089441	rs637625	A	G	358.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=1;HaplotypeScore=0.95;MQ=59.69;MQ0=0;OQ=992.46;QD=13.23;SB=-330.00	GT:AD:DP:GL:GQ	0/1:37,38:73:-124.53,-22.00,-148.03:99
-20	10089525	rs526819	C	T	411.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=82;Dels=0.00;HRun=0;HaplotypeScore=0.99;MQ=58.84;MQ0=0;OQ=1526.59;QD=17.96;SB=-694.71	GT:AD:DP:GL:GQ	0/1:41,44:82:-180.66,-24.71,-123.55:99
-20	10090764	rs670562	A	G	90.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=5.75;MQ=59.44;MQ0=0;OQ=705.16;QD=10.52;SB=-326.14	GT:AD:DP:GL:GQ	0/1:37,30:65:-93.39,-19.59,-148.34:99
-20	10090970	rs671426	T	C	386.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=59.73;MQ0=0;OQ=1093.51;QD=15.62;SB=-550.11	GT:AD:DP:GL:GQ	0/1:33,37:67:-132.81,-20.18,-125.76:99
-20	10091214	rs563455	C	T	321.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.00;HRun=0;HaplotypeScore=2.96;MQ=59.75;MQ0=0;OQ=1276.23;QD=17.02;SB=-480.51	GT:AD:DP:GL:GQ	0/1:36,39:73:-152.90,-21.99,-128.97:99
-20	10092415	rs590717	A	G	409.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1457.26;QD=14.57;SB=-743.58	GT:AD:DP:GL:GQ	0/1:51,49:100:-179.13,-30.12,-213.26:99
-20	10092927	.	G	T	0.01	FDRtranche2.00to10.00	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=1;HaplotypeScore=8.09;MQ=59.09;MQ0=0;OQ=102.52;QD=1.35;SB=110.34	GT:AD:DP:GL:GQ	0/1:58,17:57:-30.71,-17.17,-163.94:99
-20	10093923	rs2423481	T	A	501.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=59.71;MQ0=0;OQ=952.53;QD=14.65;SB=-490.92	GT:AD:DP:GL:GQ	0/1:33,32:64:-117.81,-19.28,-126.25:99
-20	10094251	rs543895	T	A	466.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=60.00;MQ0=0;OQ=1175.29;QD=18.66;SB=-397.80	GT:AD:DP:GL:GQ	0/1:26,37:59:-138.58,-17.77,-89.00:99
-20	10094582	rs56124148	A	G	315.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=65;Dels=0.00;HRun=0;HaplotypeScore=0.74;MQ=59.72;MQ0=0;OQ=736.10;QD=11.15;SB=-314.87	GT:AD:DP:GL:GQ	0/1:38,28:65:-96.47,-19.58,-152.04:99
-20	10094774	rs570383	C	T	361.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=1.97;MQ=60.00;MQ0=0;OQ=1017.49;QD=13.75;SB=-374.10	GT:AD:DP:GL:GQ	0/1:39,35:69:-125.82,-20.79,-130.93:99
-20	10095741	rs489548	A	G	80.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=68;Dels=0.00;HRun=2;HaplotypeScore=0.33;MQ=57.01;MQ0=0;OQ=943.34;QD=13.29;SB=-405.22	GT:AD:DP:GL:GQ	0/1:36,34:68:-118.10,-20.48,-142.28:99
-20	10096293	rs515940	C	T	94.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.00;HRun=2;HaplotypeScore=0.99;MQ=59.19;MQ0=0;OQ=1320.58;QD=17.61;SB=-665.71	GT:AD:DP:GL:GQ	0/1:37,38:74:-157.63,-22.29,-130.19:99
-20	10096596	rs518701	C	T	23.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.00;HRun=2;HaplotypeScore=0.16;MQ=59.03;MQ0=0;OQ=1543.46;QD=17.95;SB=-788.95	GT:AD:DP:GL:GQ	0/1:40,46:85:-183.24,-25.61,-136.84:99
-20	10096768	rs520453	A	C	398.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=59.47;MQ0=0;OQ=1343.01;QD=15.44;SB=-695.73	GT:AD:DP:GL:GQ	0/1:42,45:87:-163.78,-26.20,-154.89:99
-20	10096899	rs652086	G	T	1162.66	Indel	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.00;HRun=3;HaplotypeScore=0.89;MQ=59.76;MQ0=0;QD=14.72;SB=-335.13	GT:AD:DP:GL:GQ	0/1:39,40:78:-143.04,-23.49,-142.37:99
-20	10096933	rs652126	G	C	307.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.00;HRun=0;HaplotypeScore=0.16;MQ=59.78;MQ0=0;OQ=1416.78;QD=16.87;SB=-379.18	GT:AD:DP:GL:GQ	0/1:45,39:83:-169.97,-25.01,-193.85:99
-20	10096958	rs652494	G	A	342.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=0.97;MQ=59.79;MQ0=0;OQ=1501.31;QD=16.68;SB=-462.96	GT:AD:DP:GL:GQ	0/1:45,45:87:-179.62,-26.20,-157.70:99
-20	10097075	rs6077657	T	G	299.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.00;HRun=0;HaplotypeScore=0.67;MQ=58.69;MQ0=0;OQ=1264.80;QD=13.75;SB=-586.94	GT:AD:DP:GL:GQ	0/1:44,48:90:-156.87,-27.11,-157.64:99
-20	10097437	rs11698147	T	C	519.38	Indel	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.01;HRun=1;HaplotypeScore=8.62;MQ=55.90;MQ0=0;QD=7.75;SB=-133.24	GT:AD:DP:GL:GQ	0/1:45,21:62:-73.60,-18.38,-162.59:99
-20	10097465	.	C	T	31.87	LowQual	AC=1;AF=0.50;AN=2;DP=49;Dels=0.02;HRun=3;HaplotypeScore=12.58;MQ=57.18;MQ0=0;QD=0.61;SB=-33.97	GT:AD:DP:GL:GQ	0/1:46,5:49:-20.93,-14.46,-150.67:64.70
-20	10097626	rs665397	C	A	205.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=1.89;MQ=59.09;MQ0=0;OQ=521.22;QD=11.33;SB=-241.94	GT:AD:DP:GL:GQ	0/1:27,19:45:-68.96,-13.55,-93.68:99
-20	10097789	rs550824	T	C	40.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.00;HRun=2;HaplotypeScore=1.80;MQ=57.53;MQ0=1;OQ=609.05;QD=10.15;SB=-279.29	GT:AD:DP:GL:GQ	0/1:35,25:57:-81.36,-17.17,-136.53:99
-20	10097928	rs666732	G	A	147.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=1;HaplotypeScore=1.58;MQ=57.09;MQ0=0;OQ=647.39;QD=16.60;SB=-318.83	GT:AD:DP:GL:GQ	0/1:17,22:38:-79.48,-11.45,-61.53:99
-20	10098110	rs6108402	G	C	43.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=35;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.71;MQ0=0;OQ=639.58;QD=17.77;SB=-86.92	GT:AD:DP:GL:GQ	0/1:19,17:35:-77.79,-10.55,-73.75:99
-20	10098135	rs6108403	C	A	5.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.00;HRun=3;HaplotypeScore=0.98;MQ=59.93;MQ0=0;OQ=389.51;QD=10.25;SB=-43.38	GT:AD:DP:GL:GQ	0/1:24,14:38:-53.68,-11.44,-83.52:99
-20	10098237	.	A	T	39.55	PASS	AC=1;AF=0.50;AN=2;DP=13;Dels=0.00;HRun=1;HaplotypeScore=0.00;MQ=54.32;MQ0=0;OQ=159.94;QD=12.30;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,6:13:-23.19,-3.92,-25.88:99
-20	10098265	.	T	C	37.58	PASS	AC=1;AF=0.50;AN=2;DP=5;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=44.10;MQ0=0;OQ=64.00;QD=12.80;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,3:5:-11.19,-1.51,-7.23:57.28
-20	10098344	.	A	G	24.50	LowQual	AC=1;AF=0.50;AN=2;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=47.12;MQ0=0;QD=6.13;SB=-10.00	GT:AD:DP:GL:GQ	0/1:2,2:4:-6.94,-1.20,-8.11:57.33
-20	10098786	.	C	T	16.33	LowQual	AC=1;AF=0.50;AN=2;DP=9;Dels=0.00;HRun=0;HaplotypeScore=1.27;MQ=54.65;MQ0=0;QD=1.81;SB=-10.00	GT:AD:DP:GL:GQ	0/1:7,2:9:-7.62,-2.71,-21.38:49.06
-20	10098945	rs56176249	T	C	5.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=1;HaplotypeScore=0.73;MQ=51.33;MQ0=0;OQ=363.84;QD=17.33;SB=-10.00	GT:AD:DP:GL:GQ	0/1:8,13:20:-45.69,-6.02,-27.59:99
-20	10098987	.	C	T	11	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=51.90;MQ0=0;OQ=342.06;QD=14.87;SB=-3.99	GT:AD:DP:GL:GQ	0/1:10,13:21:-43.82,-6.33,-33.84:99
-20	10099029	rs13044987	T	C	3.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=25;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=53.87;MQ0=0;OQ=125.69;QD=4.66;SB=2.03	GT:AD:DP:GL:GQ	0/1:18,9:25:-23.39,-7.53,-70.35:99
-20	10099034	rs13043768	C	A	139.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=53.19;MQ0=0;OQ=176.63;QD=6.31;SB=-31.94	GT:AD:DP:GL:GQ	0/1:18,10:26:-28.78,-7.84,-59.75:99
-20	10099044	rs13043626	A	C	29.61	LowQual	AC=1;AF=0.50;AN=2;DB;DP=15;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=51.36;MQ0=0;QD=1.29;SB=-14.48	GT:AD:DP:GL:GQ	0/1:16,7:15:-10.76,-4.52,-43.68:62.44
-20	10099055	rs13045001	T	C	65.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=23;Dels=0.00;HRun=1;HaplotypeScore=1.00;MQ=48.67;MQ0=0;OQ=222.63;QD=7.95;SB=-64.86	GT:AD:DP:GL:GQ	0/1:16,12:23:-32.47,-6.93,-57.23:99
-20	10099079	rs13043786	C	T	16.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=31;Dels=0.00;HRun=0;HaplotypeScore=5.99;MQ=49.66;MQ0=0;OQ=370.70;QD=10.59;SB=-162.25	GT:AD:DP:GL:GQ	0/1:21,14:31:-49.70,-9.35,-56.03:99
-20	10099140	rs585009	G	T	0.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.00;HRun=5;HaplotypeScore=2.65;MQ=55.73;MQ0=0;OQ=847.58;QD=14.13;SB=-233.91	GT:AD:DP:GL:GQ	0/1:30,30:58:-105.51,-17.47,-102.15:99
-20	10099190	rs508242	G	T	210.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.47;MQ=57.42;MQ0=0;OQ=860.99;QD=13.25;SB=-270.28	GT:AD:DP:GL:GQ	0/1:33,32:62:-108.05,-18.67,-118.91:99
-20	10099220	rs585404	A	G	5.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=2;HaplotypeScore=6.00;MQ=56.96;MQ0=0;OQ=481.07;QD=10.46;SB=-187.61	GT:AD:DP:GL:GQ	0/1:25,21:43:-64.35,-12.96,-100.07:99
-20	10099250	rs585439	G	A	100.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.00;HRun=1;HaplotypeScore=1.66;MQ=56.23;MQ0=0;OQ=672.67;QD=17.70;SB=-330.34	GT:AD:DP:GL:GQ	0/1:17,21:36:-81.41,-10.86,-48.14:99
-20	10099535	rs586791	G	A	209.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.00;HRun=0;HaplotypeScore=2.83;MQ=59.28;MQ0=0;OQ=1326.40;QD=20.73;SB=-582.88	GT:AD:DP:GL:GQ	0/1:25,38:62:-157.48,-21.55,-76.17:99
-20	10099565	rs532882	C	T	44.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=2;HaplotypeScore=1.99;MQ=59.66;MQ0=0;OQ=1282.88;QD=19.15;SB=-617.46	GT:AD:DP:GL:GQ	0/1:30,37:67:-151.75,-20.18,-103.68:99
-20	10099755	rs534687	C	T	66.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.00;HRun=1;HaplotypeScore=3.91;MQ=59.00;MQ0=0;OQ=1091.00;QD=16.78;SB=-547.75	GT:AD:DP:GL:GQ	0/1:32,33:64:-131.66,-19.27,-116.96:99
-20	10099832	rs534882	A	G	477.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=58.96;MQ0=0;OQ=927.85;QD=12.89;SB=-445.10	GT:AD:DP:GL:GQ	0/1:39,33:71:-117.45,-21.39,-156.97:99

public/testdata/VariantEval/header.txt

@@ -1,14 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625

public/testdata/VariantEval/indbnp129_notindbsnp132.txt

@@ -1 +0,0 @@
-20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37

public/testdata/VariantEval/indbnp132_notindbsnp129.txt

@@ -1,2 +0,0 @@
-20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
-20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.

public/testdata/VariantEval/indels.txt

@@ -1 +0,0 @@
-20	4680094	rs112637437	CCATGGTGGTGGCTGGGGACAGCCT	C	3590.76	.	AC=12;AF=0.0625;AN=192;DB;DP=1386;Dels=0.04;HRun=1;HaplotypeScore=3.9792;MQ=57.75;MQ0=6;QD=21.89;SB=-1275.83;sumGLbyD=21.89	GT:DP:GQ:PL	0/0:28:51.14:0,51,1539	0/1:8:99:287,0,160	0/1:10:99:549,0,338

public/testdata/VariantEval/inhapmap.txt

@@ -1 +0,0 @@
-20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0

public/testdata/VariantEval/inomni.txt

@@ -1 +0,0 @@
-20	10032432	rs78089752	A	.	367.04	PASS	AC=0;AF=0.00;AN=6;DBSNP132;DP=18;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.changesAA_3=true;refseq.changesAA_4=true;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.1765A>A;refseq.codingCoordStr_2=c.1765A>A;refseq.codingCoordStr_3=c.1765A>C;refseq.codingCoordStr_4=c.1765A>C;refseq.codingCoordStr_5=c.1765A>G;refseq.codingCoordStr_6=c.1765A>G;refseq.codingCoordStr_7=c.1765A>T;refseq.codingCoordStr_8=c.1765A>T;refseq.codonCoord_1=589;refseq.codonCoord_2=589;refseq.codonCoord_3=589;refseq.codonCoord_4=589;refseq.codonCoord_5=589;refseq.codonCoord_6=589;refseq.codonCoord_7=589;refseq.codonCoord_8=589;refseq.end_1=10032432;refseq.end_2=10032432;refseq.end_3=10032432;refseq.end_4=10032432;refseq.end_5=10032432;refseq.end_6=10032432;refseq.end_7=10032432;refseq.end_8=10032432;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.functionalClass_3=missense;refseq.functionalClass_4=missense;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.haplotypeReference_3=A;refseq.haplotypeReference_4=A;refseq.haplotypeReference_5=A;refseq.haplotypeReference_6=A;refseq.haplotypeReference_7=A;refseq.haplotypeReference_8=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=2158;refseq.mrnaCoord_2=2094;refseq.mrnaCoord_3=2158;refseq.mrnaCoord_4=2094;refseq.mrnaCoord_5=2158;refseq.mrnaCoord_6=2094;refseq.mrnaCoord_7=2158;refseq.mrnaCoord_8=2094;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.I589I;refseq.proteinCoordStr_2=p.I589I;refseq.proteinCoordStr_3=p.I589L;refseq.proteinCoordStr_4=p.I589L;refseq.proteinCoordStr_5=p.I589V;refseq.proteinCoordStr_6=p.I589V;refseq.proteinCoordStr_7=p.I589F;refseq.proteinCoordStr_8=p.I589F;refseq.referenceAA_1=Ile;refseq.referenceAA_2=Ile;refseq.referenceAA_3=Ile;refseq.referenceAA_4=Ile;refseq.referenceAA_5=Ile;refseq.referenceAA_6=Ile;refseq.referenceAA_7=Ile;refseq.referenceAA_8=Ile;refseq.referenceCodon_1=ATC;refseq.referenceCodon_2=ATC;refseq.referenceCodon_3=ATC;refseq.referenceCodon_4=ATC;refseq.referenceCodon_5=ATC;refseq.referenceCodon_6=ATC;refseq.referenceCodon_7=ATC;refseq.referenceCodon_8=ATC;refseq.spliceDist_1=-106;refseq.spliceDist_2=-106;refseq.spliceDist_3=-106;refseq.spliceDist_4=-106;refseq.spliceDist_5=-106;refseq.spliceDist_6=-106;refseq.spliceDist_7=-106;refseq.spliceDist_8=-106;refseq.start_1=10032432;refseq.start_2=10032432;refseq.start_3=10032432;refseq.start_4=10032432;refseq.start_5=10032432;refseq.start_6=10032432;refseq.start_7=10032432;refseq.start_8=10032432;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Ile;refseq.variantAA_2=Ile;refseq.variantAA_3=Leu;refseq.variantAA_4=Leu;refseq.variantAA_5=Val;refseq.variantAA_6=Val;refseq.variantAA_7=Phe;refseq.variantAA_8=Phe;refseq.variantCodon_1=ATC;refseq.variantCodon_2=ATC;refseq.variantCodon_3=CTC;refseq.variantCodon_4=CTC;refseq.variantCodon_5=GTC;refseq.variantCodon_6=GTC;refseq.variantCodon_7=TTC;refseq.variantCodon_8=TTC	GT:DP:GQ:PL	0/0:5:15:0,15,175	0/0:8:24:0,24,293	0/0:5:15:0,15,182

public/testdata/VariantEval/missense.txt

@@ -1 +0,0 @@
-20	10019169	rs7260784	C	.	1193.61	PASS	AC=0;AF=0.00;AN=6;DBSNP129;DBSNP132;DP=14;HAPMAP;OMNI;refseq.changesAA_1=true;refseq.changesAA_2=true;refseq.changesAA_3=false;refseq.changesAA_4=false;refseq.changesAA_5=true;refseq.changesAA_6=true;refseq.changesAA_7=true;refseq.changesAA_8=true;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.220C>A;refseq.codingCoordStr_2=c.220C>A;refseq.codingCoordStr_3=c.220C>C;refseq.codingCoordStr_4=c.220C>C;refseq.codingCoordStr_5=c.220C>G;refseq.codingCoordStr_6=c.220C>G;refseq.codingCoordStr_7=c.220C>T;refseq.codingCoordStr_8=c.220C>T;refseq.codonCoord_1=74;refseq.codonCoord_2=74;refseq.codonCoord_3=74;refseq.codonCoord_4=74;refseq.codonCoord_5=74;refseq.codonCoord_6=74;refseq.codonCoord_7=74;refseq.codonCoord_8=74;refseq.end_1=10019169;refseq.end_2=10019169;refseq.end_3=10019169;refseq.end_4=10019169;refseq.end_5=10019169;refseq.end_6=10019169;refseq.end_7=10019169;refseq.end_8=10019169;refseq.frame_1=0;refseq.frame_2=0;refseq.frame_3=0;refseq.frame_4=0;refseq.frame_5=0;refseq.frame_6=0;refseq.frame_7=0;refseq.frame_8=0;refseq.functionalClass_1=missense;refseq.functionalClass_2=missense;refseq.functionalClass_3=silent;refseq.functionalClass_4=silent;refseq.functionalClass_5=missense;refseq.functionalClass_6=missense;refseq.functionalClass_7=missense;refseq.functionalClass_8=missense;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=C;refseq.haplotypeReference_2=C;refseq.haplotypeReference_3=C;refseq.haplotypeReference_4=C;refseq.haplotypeReference_5=C;refseq.haplotypeReference_6=C;refseq.haplotypeReference_7=C;refseq.haplotypeReference_8=C;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.inCodingRegion_3=true;refseq.inCodingRegion_4=true;refseq.inCodingRegion_5=true;refseq.inCodingRegion_6=true;refseq.inCodingRegion_7=true;refseq.inCodingRegion_8=true;refseq.mrnaCoord_1=613;refseq.mrnaCoord_2=549;refseq.mrnaCoord_3=613;refseq.mrnaCoord_4=549;refseq.mrnaCoord_5=613;refseq.mrnaCoord_6=549;refseq.mrnaCoord_7=613;refseq.mrnaCoord_8=549;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.positionType_3=CDS;refseq.positionType_4=CDS;refseq.positionType_5=CDS;refseq.positionType_6=CDS;refseq.positionType_7=CDS;refseq.positionType_8=CDS;refseq.proteinCoordStr_1=p.P74T;refseq.proteinCoordStr_2=p.P74T;refseq.proteinCoordStr_3=p.P74P;refseq.proteinCoordStr_4=p.P74P;refseq.proteinCoordStr_5=p.P74A;refseq.proteinCoordStr_6=p.P74A;refseq.proteinCoordStr_7=p.P74S;refseq.proteinCoordStr_8=p.P74S;refseq.referenceAA_1=Pro;refseq.referenceAA_2=Pro;refseq.referenceAA_3=Pro;refseq.referenceAA_4=Pro;refseq.referenceAA_5=Pro;refseq.referenceAA_6=Pro;refseq.referenceAA_7=Pro;refseq.referenceAA_8=Pro;refseq.referenceCodon_1=CCT;refseq.referenceCodon_2=CCT;refseq.referenceCodon_3=CCT;refseq.referenceCodon_4=CCT;refseq.referenceCodon_5=CCT;refseq.referenceCodon_6=CCT;refseq.referenceCodon_7=CCT;refseq.referenceCodon_8=CCT;refseq.spliceDist_1=-127;refseq.spliceDist_2=-127;refseq.spliceDist_3=-127;refseq.spliceDist_4=-127;refseq.spliceDist_5=-127;refseq.spliceDist_6=-127;refseq.spliceDist_7=-127;refseq.spliceDist_8=-127;refseq.start_1=10019169;refseq.start_2=10019169;refseq.start_3=10019169;refseq.start_4=10019169;refseq.start_5=10019169;refseq.start_6=10019169;refseq.start_7=10019169;refseq.start_8=10019169;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+;refseq.variantAA_1=Thr;refseq.variantAA_2=Thr;refseq.variantAA_3=Pro;refseq.variantAA_4=Pro;refseq.variantAA_5=Ala;refseq.variantAA_6=Ala;refseq.variantAA_7=Ser;refseq.variantAA_8=Ser;refseq.variantCodon_1=ACT;refseq.variantCodon_2=ACT;refseq.variantCodon_3=CCT;refseq.variantCodon_4=CCT;refseq.variantCodon_5=GCT;refseq.variantCodon_6=GCT;refseq.variantCodon_7=TCT;refseq.variantCodon_8=TCT	GT:DP:GQ:PL	0/0:4:12:0,12,138	0/0:6:18:0,18,211	0/0:4:12:0,12,144

public/testdata/VariantEval/one_transition_and_one_transversion.vcf

@@ -1,6 +0,0 @@
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0

public/testdata/VariantEval/pacbio.hg19.intervals

@@ -1,61 +0,0 @@
-20:1408612-1410111
-20:2156456-2157954
-20:2449737-2451239
-20:3152386-3153891
-20:4756022-4757518
-20:5904863-5906362
-20:6229017-6230516
-20:6348326-6349839
-20:6468951-6470450
-20:8669911-8671404
-20:9090417-9091931
-20:10339474-10340969
-20:11964411-11965911
-20:12189566-12191074
-20:15237801-15239305
-20:15965572-15967061
-20:16075651-16077128
-20:16990896-16992393
-20:23364965-23366475
-20:23710044-23711543
-20:23773906-23775416
-20:24317459-24318954
-20:25830118-25831610
-20:25890727-25892236
-20:25904830-25906332
-20:26130086-26133738
-20:26142111-26144870
-20:26145383-26146891
-20:26148300-26149799
-20:26207333-26208839
-20:26210063-26211564
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public/testdata/VariantEval/pacbio.ts.recalibrated.vcf

@@ -1,566 +0,0 @@
-##fileformat=VCFv4.0
-##FILTER=<ID=HARD_TO_VALIDATE,Description="MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1">
-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
-##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
-##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
-##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="log10-scaled probability of variant being true under the trained gaussian mixture model">
-##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.recal.bam] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/Q-27737@node1309-1-sg/temp-1/scatter.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.rod downsampling_type=null downsample_to_fraction=null downsample_to_coverage=250 baq=RECALCULATE baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false genotype_likelihoods_model=SNP p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotype=false output_all_callable_bases=false standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 trigger_min_confidence_threshold_for_calling=30.0 trigger_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=NA12878 min_base_quality_score=10 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.5 get_indel_alleles_from_vcf=false min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub verbose_mode=null metrics_file=null annotation=[]"
-##VariantFiltration="analysis_type=VariantFiltration input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/Q-27737@node1309-2-sg/temp-1/scatter.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/pacbio.raw.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filterExpression=[MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1] filterName=[HARD_TO_VALIDATE] genotypeFilterExpression=[] genotypeFilterName=[] clusterSize=3 clusterWindowSize=0 maskName=Mask missingValuesInExpressionsShouldEvaluateAsFailing=false"
-##VariantRecalibrator="analysis_type=VariantRecalibrator input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=[/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.hg19.intervals] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_g1k_v37.fasta rodBind=[/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf, /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf, /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf, /humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/pacbio.filtered.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.rod downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false cluster_file=/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/pacbio.clusters tranches_file=/humgen/gsa-scr1/carneiro/prj/pacbio/analysis/snps/amplicon/pacbio.ts.tranches out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub target_titv=1.8 backOff=1.3 ignore_all_input_filters=false priorNovel=2.0 priorDBSNP=2.0 priorHapMap=2.0 prior1KG=2.0 path_to_Rscript=Rscript path_to_resources=R/ singleton_fp_rate=0.5 max_ac_prior=0.99 dontTrustACField=false qual=0.0 debugFile=null selectionMetric=TRUTH_SENSITIVITY use_annotation=null"
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	1408919	rs6074626	C	T	410.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.06;HRun=1;HaplotypeScore=114.0668;MQ=60.00;MQ0=0;QD=5.33;SB=-173.00;VQSLOD=-1.3245;sumGLbyD=5.72	GT:AD:DP:GQ:PL	0/1:41,29:58:99:440,0,594
-20	1409435	rs4814243	G	A	2219.30	PASS	AC=2;AF=1.00;AN=2;DB;DP=175;Dels=0.01;HRun=0;HaplotypeScore=161.5624;MQ=60.00;MQ0=0;QD=12.68;SB=-808.23;VQSLOD=-2.4575;sumGLbyD=12.87	GT:AD:DP:GQ:PL	1/1:9,139:109:99:2252,161,0
-20	1409567	rs4814244	A	G	1734.11	PASS	AC=2;AF=1.00;AN=2;DB;DP=153;Dels=0.22;HRun=1;HaplotypeScore=505.1471;MQ=60.00;MQ0=0;QD=11.33;SB=-772.45;VQSLOD=-1.6321;sumGLbyD=11.55	GT:AD:DP:GQ:PL	1/1:6,111:82:99:1767,193,0
-20	1409612	.	T	A	579.26	PASS	AC=1;AF=0.50;AN=2;DP=148;Dels=0.16;HRun=2;HaplotypeScore=372.8065;MQ=60.00;MQ0=0;QD=3.91;SB=-155.28;VQSLOD=-2.1200;sumGLbyD=4.12	GT:AD:DP:GQ:PL	0/1:74,45:87:99:609,0,883
-20	1409757	rs6134916	C	T	252.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=91;Dels=0.08;HRun=1;HaplotypeScore=176.9395;MQ=60.00;MQ0=0;QD=2.77;SB=-123.36;VQSLOD=-1.3707;sumGLbyD=3.10	GT:AD:DP:GQ:PL	0/1:54,24:58:99:282,0,673
-20	2156688	rs34950074	A	G	160.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.20;HRun=3;HaplotypeScore=311.7372;MQ=60.00;MQ0=0;QD=1.98;SB=-59.56;VQSLOD=-3.8407;sumGLbyD=2.35	GT:AD:DP:GQ:PL	0/1:41,19:52:99:191,0,699
-20	2157130	rs6137228	G	A	1074.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=241;Dels=0.08;HRun=0;HaplotypeScore=495.1212;MQ=60.00;MQ0=0;QD=4.46;SB=-543.36;VQSLOD=-1.0631;sumGLbyD=4.58	GT:AD:DP:GQ:PL	0/1:129,88:161:99:1105,0,1376
-20	2157596	rs41308621	G	A	37.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=115;Dels=0.16;HRun=0;HaplotypeScore=356.4928;MQ=60.00;MQ0=0;QD=0.33;SB=7.11;VQSLOD=-2.1065;sumGLbyD=0.59	GT:AD:DP:GQ:PL	0/1:67,29:45:67.65:68,0,574
-20	2450144	rs6106763	T	C	384.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=161;Dels=0.09;HRun=1;HaplotypeScore=350.4436;MQ=60.00;MQ0=0;QD=2.39;SB=-164.46;VQSLOD=-1.2122;sumGLbyD=2.57	GT:AD:DP:GQ:PL	0/1:93,48:111:99:414,0,1456
-20	2450235	rs6138180	A	T	646.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=211;Dels=0.14;HRun=0;HaplotypeScore=566.4039;MQ=60.00;MQ0=0;QD=3.06;SB=-286.95;VQSLOD=-1.6466;sumGLbyD=3.21	GT:AD:DP:GQ:PL	0/1:105,68:127:99:677,0,1540
-20	2450669	rs6049283	C	A	859.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=213;DS;Dels=0.00;HRun=0;HaplotypeScore=268.1049;MQ=60.00;MQ0=0;QD=4.04;SB=-396.35;VQSLOD=-0.4104;sumGLbyD=4.18	GT:AD:DP:GQ:PL	0/1:124,78:126:99:890,0,1027
-20	3152793	rs6051617	T	C	196.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.02;HRun=0;HaplotypeScore=156.2935;MQ=60.00;MQ0=0;QD=1.93;SB=-54.81;VQSLOD=-1.0530;sumGLbyD=2.22	GT:AD:DP:GQ:PL	0/1:71,25:74:99:227,0,1001
-20	3153236	.	C	G	304.30	PASS	AC=1;AF=0.50;AN=2;DP=119;Dels=0.16;HRun=1;HaplotypeScore=320.3893;MQ=60.00;MQ0=0;QD=2.56;SB=-155.71;VQSLOD=-1.3115;sumGLbyD=2.81	GT:AD:DP:GQ:PL	0/1:63,30:69:99:334,0,819
-20	3153503	rs55785911	G	A	88.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.11;HRun=1;HaplotypeScore=160.1451;MQ=60.00;MQ0=0;QD=1.23;SB=-51.31;VQSLOD=-2.1979;sumGLbyD=1.65	GT:AD:DP:GQ:PL	0/1:44,18:42:99:119,0,606
-20	3153605	.	C	T	151.39	PASS	AC=1;AF=0.50;AN=2;DP=60;Dels=0.15;HRun=1;HaplotypeScore=161.0277;MQ=60.00;MQ0=0;QD=2.52;SB=-20.11;VQSLOD=-2.1881;sumGLbyD=3.02	GT:AD:DP:GQ:PL	0/1:31,19:32:99:181,0,388
-20	4756391	rs2422967	T	C	266.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=177;Dels=0.15;HRun=3;HaplotypeScore=562.1195;MQ=60.00;MQ0=0;QD=1.51;SB=-15.41;VQSLOD=-5.2491;sumGLbyD=1.67	GT:AD:DP:GQ:PL	0/1:112,33:115:99:296,0,1675
-20	4756509	rs6052868	A	G	509.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=250;DS;Dels=0.17;HRun=3;HaplotypeScore=748.4880;MQ=60.00;MQ0=0;QD=2.04;SB=-264.37;VQSLOD=-2.4325;sumGLbyD=2.16	GT:AD:DP:GQ:PL	0/1:153,49:168:99:539,0,2447
-20	4756691	rs7272323	G	C	624.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=248;DS;Dels=0.00;HRun=0;HaplotypeScore=196.5430;MQ=60.00;MQ0=0;QD=2.52;SB=-163.80;VQSLOD=-0.2919;sumGLbyD=2.64	GT:AD:DP:GQ:PL	0/1:175,68:164:99:655,0,1886
-20	5905472	rs236154	G	T	764.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=181;Dels=0.00;HRun=0;HaplotypeScore=202.1957;MQ=60.00;MQ0=0;QD=4.23;SB=-330.33;VQSLOD=-0.4780;sumGLbyD=4.39	GT:AD:DP:GQ:PL	0/1:111,68:100:99:795,0,873
-20	5905550	rs236155	G	A	1050.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.02;HRun=0;HaplotypeScore=173.3788;MQ=60.00;MQ0=0;QD=6.14;SB=-462.20;VQSLOD=-1.2994;sumGLbyD=6.32	GT:AD:DP:GQ:PL	0/1:79,82:131:99:1080,0,1181
-20	5905779	rs2821	C	A	550.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=158;Dels=0.05;HRun=0;HaplotypeScore=266.6426;MQ=60.00;MQ0=0;QD=3.48;SB=-201.81;VQSLOD=-0.4809;sumGLbyD=3.67	GT:AD:DP:GQ:PL	0/1:90,51:108:99:580,0,1342
-20	5906092	rs236157	G	A	195.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;Dels=0.04;HRun=0;HaplotypeScore=129.6758;MQ=60.00;MQ0=0;QD=2.76;SB=-84.66;VQSLOD=-0.6734;sumGLbyD=3.18	GT:AD:DP:GQ:PL	0/1:39,25:45:99:226,0,542
-20	5906098	rs10454160	A	C	79.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.13;HRun=0;HaplotypeScore=191.3074;MQ=60.00;MQ0=0;QD=1.14;SB=15.70;VQSLOD=-1.8202;sumGLbyD=1.57	GT:AD:DP:GQ:PL	0/1:42,17:45:99:110,0,679
-20	6229263	rs6054023	T	C	393.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.05;HRun=0;HaplotypeScore=143.3775;MQ=60.00;MQ0=0;QD=3.86;SB=-117.41;VQSLOD=-0.4836;sumGLbyD=4.15	GT:AD:DP:GQ:PL	0/1:64,31:77:99:424,0,859
-20	6229282	rs6054024	A	C	276.91	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.11;HRun=0;HaplotypeScore=239.9223;MQ=60.00;MQ0=0;QD=2.71;SB=-129.32;VQSLOD=-0.4773;sumGLbyD=3.01	GT:AD:DP:GQ:PL	0/1:58,27:65:99:307,0,790
-20	6229367	rs55708193	C	A	284.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=116;Dels=0.00;HRun=0;HaplotypeScore=100.3668;MQ=60.00;MQ0=0;QD=2.46;SB=9.48;VQSLOD=-1.8120;sumGLbyD=2.71	GT:AD:DP:GQ:PL	0/1:75,31:76:99:315,0,984
-20	6229867	rs6054027	C	A	1024.03	PASS	AC=1;AF=0.50;AN=2;DB;DP=224;Dels=0.04;HRun=0;HaplotypeScore=254.7872;MQ=60.00;MQ0=0;QD=4.57;SB=-449.69;VQSLOD=-0.6894;sumGLbyD=4.71	GT:AD:DP:GQ:PL	0/1:120,90:160:99:1054,0,1742
-20	6230133	rs6038393	C	T	271.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=142;Dels=0.00;HRun=0;HaplotypeScore=102.9663;MQ=60.00;MQ0=0;QD=1.91;SB=-85.43;VQSLOD=-1.2156;sumGLbyD=2.12	GT:AD:DP:GQ:PL	0/1:95,43:79:99:302,0,1065
-20	6230247	rs6085447	T	A	341.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.04;HRun=2;HaplotypeScore=109.4730;MQ=60.00;MQ0=0;QD=3.49;SB=-99.61;VQSLOD=-2.3533;sumGLbyD=3.79	GT:AD:DP:GQ:PL	0/1:51,39:62:99:372,0,694
-20	6469312	rs4441551	C	G	323.38	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;Dels=0.11;HRun=1;HaplotypeScore=193.6133;MQ=60.00;MQ0=0;QD=3.63;SB=-89.68;VQSLOD=-1.4989;sumGLbyD=3.97	GT:AD:DP:GQ:PL	0/1:49,28:70:99:353,0,833
-20	6469515	rs62200027	G	A	808.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.03;HRun=0;HaplotypeScore=175.1223;MQ=60.00;MQ0=0;QD=4.35;SB=-356.55;VQSLOD=-0.6362;sumGLbyD=4.51	GT:AD:DP:GQ:PL	0/1:104,67:137:99:839,0,1240
-20	6469596	rs17721822	G	A	895.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=212;Dels=0.00;HRun=0;HaplotypeScore=197.3459;MQ=60.00;MQ0=0;QD=4.22;SB=-354.06;VQSLOD=-0.5273;sumGLbyD=4.37	GT:AD:DP:GQ:PL	0/1:126,80:147:99:926,0,1588
-20	6470035	rs928203	T	C	414.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=130;Dels=0.00;HRun=0;HaplotypeScore=127.3479;MQ=60.00;MQ0=0;QD=3.19;SB=-135.40;VQSLOD=-0.3583;sumGLbyD=3.42	GT:AD:DP:GQ:PL	0/1:74,43:77:99:445,0,890
-20	6470094	rs2326788	G	A	478.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=113;Dels=0.01;HRun=0;HaplotypeScore=94.4097;MQ=60.00;MQ0=0;QD=4.23;SB=-145.71;VQSLOD=-0.5743;sumGLbyD=4.50	GT:AD:DP:GQ:PL	0/1:60,44:69:99:508,0,506
-20	6470104	rs2326789	G	A	358.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.03;HRun=0;HaplotypeScore=119.9128;MQ=60.00;MQ0=0;QD=3.23;SB=-119.02;VQSLOD=-0.4560;sumGLbyD=3.50	GT:AD:DP:GQ:PL	0/1:61,41:69:99:389,0,613
-20	6470265	rs928202	A	G	225.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.18;HRun=2;HaplotypeScore=279.3012;MQ=60.00;MQ0=0;QD=2.66;SB=-42.82;VQSLOD=-2.0778;sumGLbyD=3.01	GT:AD:DP:GQ:PL	0/1:44,21:53:99:256,0,596
-20	8669964	rs6056014	T	G	273.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=0;HaplotypeScore=35.4095;MQ=60.00;MQ0=0;QD=10.13;SB=-102.32;VQSLOD=-2.3500;sumGLbyD=11.24	GT:AD:DP:GQ:PL	0/1:4,21:20:37.87:303,0,38
-20	8670065	rs6056015	T	C	108.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.03;HRun=0;HaplotypeScore=49.9322;MQ=60.00;MQ0=0;QD=3.19;SB=-10.17;VQSLOD=-1.8803;sumGLbyD=4.07	GT:AD:DP:GQ:PL	0/1:13,19:12:50.94:138,0,51
-20	8670241	rs6039235	T	G	208.30	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.03;HRun=0;HaplotypeScore=40.0000;MQ=60.00;MQ0=0;QD=6.31;SB=-92.44;VQSLOD=-1.7385;sumGLbyD=7.22	GT:AD:DP:GQ:PL	0/1:11,19:16:46.86:238,0,47
-20	8670262	rs6056017	T	C	33.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=38;Dels=0.08;HRun=0;HaplotypeScore=52.5865;MQ=60.00;MQ0=0;QD=0.88;SB=5.22;VQSLOD=-3.0319;sumGLbyD=1.66	GT:AD:DP:GQ:PL	0/1:24,9:26:63.26:63,0,383
-20	8670293	rs6056018	A	G	424.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=45;Dels=0.00;HRun=0;HaplotypeScore=28.3805;MQ=60.00;MQ0=0;QD=9.44;SB=-177.24;VQSLOD=-1.6125;sumGLbyD=10.11	GT:AD:DP:GQ:PL	0/1:17,28:30:59.88:455,0,60
-20	8670437	rs6039236	T	G	360.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;Dels=0.31;HRun=1;HaplotypeScore=282.2481;MQ=60.00;MQ0=0;QD=5.91;SB=-98.53;VQSLOD=-1.6269;sumGLbyD=6.40	GT:AD:DP:GQ:PL	0/1:15,25:26:14.11:390,0,14
-20	8670714	rs6039237	C	T	1053.27	PASS	AC=2;AF=1.00;AN=2;DB;DP=78;Dels=0.05;HRun=0;HaplotypeScore=92.3301;MQ=60.00;MQ0=0;QD=13.50;SB=-122.38;VQSLOD=-5.3130;sumGLbyD=13.93	GT:AD:DP:GQ:PL	1/1:7,61:56:49.10:1086,49,0
-20	8670868	rs6056019	T	C	955.12	PASS	AC=2;AF=1.00;AN=2;DB;DP=105;Dels=0.21;HRun=1;HaplotypeScore=381.2305;MQ=60.00;MQ0=0;QD=9.10;SB=-286.55;VQSLOD=-1.7128;sumGLbyD=9.41	GT:AD:DP:GQ:PL	1/1:13,66:54:99:988,156,0
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-20	9091235	rs6140861	T	C	898.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=249;DS;Dels=0.05;HRun=0;HaplotypeScore=321.1324;MQ=60.00;MQ0=0;QD=3.61;SB=-444.67;VQSLOD=-0.5471;sumGLbyD=3.73	GT:AD:DP:GQ:PL	0/1:154,78:168:99:928,0,1928
-20	10339646	rs6104584	C	T	144.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;Dels=0.15;HRun=0;HaplotypeScore=126.6722;MQ=60.00;MQ0=0;QD=3.08;SB=-64.83;VQSLOD=-0.8031;sumGLbyD=3.72	GT:AD:DP:GQ:PL	0/1:20,18:28:99:175,0,269
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-20	10340174	rs2423495	T	C	620.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=225;Dels=0.00;HRun=0;HaplotypeScore=206.2693;MQ=60.00;MQ0=0;QD=2.76;SB=-280.07;VQSLOD=-0.4161;sumGLbyD=2.89	GT:AD:DP:GQ:PL	0/1:137,78:158:99:651,0,1880
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-20	10340311	rs6133879	C	T	741.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=223;Dels=0.09;HRun=1;HaplotypeScore=361.5022;MQ=60.00;MQ0=0;QD=3.33;SB=-359.01;VQSLOD=-1.7772;sumGLbyD=3.46	GT:AD:DP:GQ:PL	0/1:129,67:151:99:772,0,1510
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-20	15237847	rs4813173	C	T	489.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=111;Dels=0.00;HRun=0;HaplotypeScore=101.9912;MQ=60.00;MQ0=0;QD=4.41;SB=-235.03;VQSLOD=-0.4984;sumGLbyD=4.68	GT:AD:DP:GQ:PL	0/1:67,41:90:99:519,0,1030
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-20	15237936	rs16995476	C	T	449.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=128;Dels=0.09;HRun=0;HaplotypeScore=256.3643;MQ=60.00;MQ0=0;QD=3.51;SB=-154.36;VQSLOD=-0.5877;sumGLbyD=3.75	GT:AD:DP:GQ:PL	0/1:67,41:91:99:480,0,1092
-20	15238054	.	A	G	732.20	PASS	AC=1;AF=0.50;AN=2;DP=148;Dels=0.00;HRun=1;HaplotypeScore=114.2514;MQ=60.00;MQ0=0;QD=4.95;SB=-200.83;VQSLOD=-1.4056;sumGLbyD=5.15	GT:AD:DP:GQ:PL	0/1:83,58:112:99:762,0,1118
-20	15238074	rs16995477	G	T	465.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.01;HRun=1;HaplotypeScore=115.2342;MQ=60.00;MQ0=0;QD=3.06;SB=-215.17;VQSLOD=-1.3880;sumGLbyD=3.26	GT:AD:DP:GQ:PL	0/1:96,53:113:99:496,0,1347
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-20	15966230	rs2095851	T	C	763.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=249;DS;Dels=0.03;HRun=0;HaplotypeScore=253.1538;MQ=60.00;MQ0=0;QD=3.07;SB=-362.33;VQSLOD=-0.5590;sumGLbyD=3.19	GT:AD:DP:GQ:PL	0/1:136,97:169:99:794,0,1960
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-20	16991685	rs11907778	C	G	1080.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=248;DS;Dels=0.04;HRun=0;HaplotypeScore=312.7000;MQ=60.00;MQ0=0;QD=4.36;SB=-490.00;VQSLOD=-0.6402;sumGLbyD=4.48	GT:AD:DP:GQ:PL	0/1:136,90:177:99:1111,0,1930
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-20	23711018	rs8121966	C	T	397.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=86;Dels=0.06;HRun=1;HaplotypeScore=158.7980;MQ=60.00;MQ0=0;QD=4.63;SB=-154.75;VQSLOD=-1.1940;sumGLbyD=4.97	GT:AD:DP:GQ:PL	0/1:47,34:50:99:428,0,410
-20	23711487	rs4571120	G	T	54.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=33;Dels=0.03;HRun=0;HaplotypeScore=46.5484;MQ=60.00;MQ0=0;QD=1.66;SB=-17.71;VQSLOD=-2.4515;sumGLbyD=2.57	GT:AD:DP:GQ:PL	0/1:24,7:15:84.85:85,0,134
-20	23774000	rs4437030	C	T	238.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=74.1243;MQ=60.00;MQ0=0;QD=5.41;SB=-115.18;VQSLOD=-1.3118;sumGLbyD=6.09	GT:AD:DP:GQ:PL	0/1:10,30:17:36.74:268,0,37
-20	23774006	rs5001319	G	T	362.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=44;Dels=0.00;HRun=0;HaplotypeScore=63.9971;MQ=60.00;MQ0=0;QD=8.25;SB=-159.50;VQSLOD=-1.1912;sumGLbyD=8.95	GT:AD:DP:GQ:PL	0/1:11,33:23:1.40:392,0,1
-20	23774010	rs5001318	A	T	332.22	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.36;HRun=0;HaplotypeScore=175.4995;MQ=60.00;MQ0=0;QD=7.55;SB=-175.74;VQSLOD=-0.9172;sumGLbyD=8.30	GT:AD:DP:GQ:PL	1/1:1,26:16:44.91:365,45,0
-20	23774011	rs5001317	A	C	253.54	PASS	AC=2;AF=1.00;AN=2;DB;DP=44;Dels=0.25;HRun=0;HaplotypeScore=163.6677;MQ=60.00;MQ0=0;QD=5.76;SB=-122.72;VQSLOD=-0.8453;sumGLbyD=6.51	GT:AD:DP:GQ:PL	1/1:3,26:19:29.80:287,30,0
-20	23774050	rs4438551	A	G	396.98	PASS	AC=2;AF=1.00;AN=2;DB;DP=46;Dels=0.22;HRun=1;HaplotypeScore=169.2448;MQ=60.00;MQ0=0;QD=8.63;SB=-168.21;VQSLOD=-1.2552;sumGLbyD=9.35	GT:AD:DP:GQ:PL	1/1:2,31:28:34.61:430,35,0
-20	23774138	rs4591413	C	T	177.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.13;HRun=0;HaplotypeScore=151.2344;MQ=60.00;MQ0=0;QD=3.42;SB=-14.98;VQSLOD=-1.3708;sumGLbyD=4.00	GT:AD:DP:GQ:PL	0/1:27,16:29:99:208,0,253
-20	23774560	rs6036534	A	G	362.62	PASS	AC=2;AF=1.00;AN=2;DB;DP=77;Dels=0.26;HRun=1;HaplotypeScore=266.6065;MQ=60.00;MQ0=0;QD=4.71;SB=-176.70;VQSLOD=-0.8631;sumGLbyD=5.13	GT:AD:DP:GQ:PL	1/1:14,39:29:6.83:394,7,0
-20	24317503	.	T	C	266.97	PASS	AC=1;AF=0.50;AN=2;DP=102;Dels=0.11;HRun=0;HaplotypeScore=239.6208;MQ=60.00;MQ0=0;QD=2.62;SB=-58.22;VQSLOD=-0.9783;sumGLbyD=2.91	GT:AD:DP:GQ:PL	0/1:53,35:78:99:297,0,942
-20	24317910	rs8116738	G	A	1177.87	PASS	AC=1;AF=0.50;AN=2;DB;DP=235;Dels=0.11;HRun=0;HaplotypeScore=555.7653;MQ=60.00;MQ0=0;QD=5.01;SB=-462.34;VQSLOD=-1.4874;sumGLbyD=5.14	GT:AD:DP:GQ:PL	0/1:109,98:153:99:1208,0,1288
-20	24318040	rs62193423	G	A	824.11	PASS	AC=1;AF=0.50;AN=2;DB;DP=246;DS;Dels=0.00;HRun=1;HaplotypeScore=167.1432;MQ=60.00;MQ0=0;QD=3.35;SB=-342.01;VQSLOD=-1.6522;sumGLbyD=3.47	GT:AD:DP:GQ:PL	0/1:157,82:168:99:854,0,1981
-20	24318376	rs6049609	C	G	469.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=222;DS;Dels=0.31;HRun=1;HaplotypeScore=1127.0438;MQ=60.00;MQ0=0;QD=2.12;SB=-244.24;VQSLOD=-5.0193;sumGLbyD=2.25	GT:AD:DP:GQ:PL	0/1:107,44:83:99:500,0,858
-20	25830393	rs34770871	G	C	68.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=62;Dels=0.03;HRun=0;HaplotypeScore=108.5637;MQ=60.00;MQ0=0;QD=1.10;SB=-9.01;VQSLOD=-2.1580;sumGLbyD=1.58	GT:AD:DP:GQ:PL	0/1:43,15:45:98.15:98,0,698
-20	25830541	.	T	C	58.90	PASS	AC=1;AF=0.50;AN=2;DP=87;Dels=0.07;HRun=0;HaplotypeScore=198.9685;MQ=60.00;MQ0=0;QD=0.68;SB=-38.39;VQSLOD=-1.6112;sumGLbyD=1.02	GT:AD:DP:GQ:PL	0/1:52,21:56:88.89:89,0,907
-20	25830542	.	G	A	60.16	PASS	AC=1;AF=0.50;AN=2;DP=88;Dels=0.08;HRun=0;HaplotypeScore=221.8586;MQ=60.00;MQ0=0;QD=0.68;SB=-43.46;VQSLOD=-1.5310;sumGLbyD=1.02	GT:AD:DP:GQ:PL	0/1:55,23:60:90.15:90,0,936
-20	25830566	.	T	C	118.82	PASS	AC=1;AF=0.50;AN=2;DP=105;Dels=0.05;HRun=1;HaplotypeScore=124.6832;MQ=60.00;MQ0=0;QD=1.13;SB=-26.82;VQSLOD=-2.5849;sumGLbyD=1.42	GT:AD:DP:GQ:PL	0/1:76,21:76:99:149,0,1139
-20	25830625	.	A	T	184.39	PASS	AC=1;AF=0.50;AN=2;DP=131;Dels=0.15;HRun=2;HaplotypeScore=440.3007;MQ=60.00;MQ0=0;QD=1.41;SB=-3.26;VQSLOD=-3.2273;sumGLbyD=1.64	GT:AD:DP:GQ:PL	0/1:76,32:81:99:214,0,1201
-20	25830672	.	A	G	290.25	PASS	AC=1;AF=0.50;AN=2;DP=141;Dels=0.06;HRun=0;HaplotypeScore=263.1804;MQ=60.00;MQ0=0;QD=2.06;SB=-62.43;VQSLOD=-1.0713;sumGLbyD=2.27	GT:AD:DP:GQ:PL	0/1:84,43:109:99:320,0,1443
-20	25830711	.	G	A	260.16	PASS	AC=1;AF=0.50;AN=2;DP=151;Dels=0.02;HRun=0;HaplotypeScore=170.7460;MQ=60.00;MQ0=0;QD=1.72;SB=-131.24;VQSLOD=-0.7738;sumGLbyD=1.92	GT:AD:DP:GQ:PL	0/1:113,33:86:99:290,0,1149
-20	25830827	.	T	C	111.56	PASS	AC=1;AF=0.50;AN=2;DP=183;Dels=0.05;HRun=0;HaplotypeScore=284.4761;MQ=60.00;MQ0=0;QD=0.61;SB=-66.54;VQSLOD=-1.5058;sumGLbyD=0.77	GT:AD:DP:GQ:PL	0/1:143,29:124:99:142,0,1947
-20	25830880	rs62214075	C	T	781.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=179;Dels=0.03;HRun=0;HaplotypeScore=164.5268;MQ=60.00;MQ0=0;QD=4.37;SB=-394.62;VQSLOD=-0.8159;sumGLbyD=4.53	GT:AD:DP:GQ:PL	0/1:98,67:130:99:812,0,1459
-20	25830904	rs62214076	A	G	275.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=180;Dels=0.28;HRun=4;HaplotypeScore=838.1565;MQ=60.00;MQ0=0;QD=1.53;SB=-134.33;VQSLOD=-4.7772;sumGLbyD=1.70	GT:AD:DP:GQ:PL	0/1:90,32:95:99:306,0,1397
-20	25830911	rs62214077	A	G	424.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=180;Dels=0.01;HRun=2;HaplotypeScore=261.9943;MQ=60.00;MQ0=0;QD=2.36;SB=-136.12;VQSLOD=-1.6861;sumGLbyD=2.53	GT:AD:DP:GQ:PL	0/1:135,39:124:99:455,0,1643
-20	25830979	.	T	C	81.16	PASS	AC=1;AF=0.50;AN=2;DP=178;Dels=0.04;HRun=0;HaplotypeScore=250.4914;MQ=60.00;MQ0=0;QD=0.46;SB=-38.42;VQSLOD=-1.5963;sumGLbyD=0.62	GT:AD:DP:GQ:PL	0/1:138,30:114:99:111,0,1856
-20	25830980	.	G	A	66.95	PASS	AC=1;AF=0.50;AN=2;DP=177;Dels=0.01;HRun=1;HaplotypeScore=190.2950;MQ=60.00;MQ0=0;QD=0.38;SB=-8.86;VQSLOD=-2.8271;sumGLbyD=0.55	GT:AD:DP:GQ:PL	0/1:144,27:117:96.95:97,0,1937
-20	25831141	rs62214080	T	C	252.43	PASS	AC=1;AF=0.50;AN=2;DB;DP=114;Dels=0.02;HRun=0;HaplotypeScore=134.2196;MQ=60.00;MQ0=0;QD=2.21;SB=-129.40;VQSLOD=-0.6541;sumGLbyD=2.48	GT:AD:DP:GQ:PL	0/1:73,34:77:99:282,0,1052
-20	25831185	.	C	T	201.55	PASS	AC=1;AF=0.50;AN=2;DP=107;Dels=0.08;HRun=2;HaplotypeScore=221.7598;MQ=60.00;MQ0=0;QD=1.88;SB=-98.55;VQSLOD=-1.9279;sumGLbyD=2.16	GT:AD:DP:GQ:PL	0/1:62,28:70:99:232,0,930
-20	25831281	.	T	C	202.32	PASS	AC=1;AF=0.50;AN=2;DP=79;Dels=0.04;HRun=0;HaplotypeScore=93.4892;MQ=60.00;MQ0=0;QD=2.56;SB=-75.66;VQSLOD=-1.0129;sumGLbyD=2.94	GT:AD:DP:GQ:PL	0/1:44,30:47:99:232,0,590
-20	25831364	.	C	G	190.66	PASS	AC=1;AF=0.50;AN=2;DP=67;Dels=0.03;HRun=0;HaplotypeScore=100.7710;MQ=60.00;MQ0=0;QD=2.85;SB=-95.18;VQSLOD=-0.7488;sumGLbyD=3.29	GT:AD:DP:GQ:PL	0/1:37,27:40:99:221,0,423
-20	25831374	.	A	T	93.18	PASS	AC=1;AF=0.50;AN=2;DP=67;Dels=0.03;HRun=0;HaplotypeScore=153.4111;MQ=60.00;MQ0=0;QD=1.39;SB=-5.55;VQSLOD=-1.7101;sumGLbyD=1.84	GT:AD:DP:GQ:PL	0/1:43,21:37:99:123,0,519
-20	25831381	.	A	C	121.34	PASS	AC=1;AF=0.50;AN=2;DP=67;Dels=0.19;HRun=1;HaplotypeScore=241.3830;MQ=60.00;MQ0=0;QD=1.81;SB=-65.36;VQSLOD=-1.8072;sumGLbyD=2.26	GT:AD:DP:GQ:PL	0/1:38,14:38:99:151,0,502
-20	25831383	rs34974769	C	T	44.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.01;HRun=1;HaplotypeScore=99.8162;MQ=60.00;MQ0=0;QD=0.66;SB=-35.71;VQSLOD=-2.9229;sumGLbyD=1.11	GT:AD:DP:GQ:PL	0/1:52,14:41:74.39:74,0,626
-20	25831418	.	G	C	119.94	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.00;HRun=0;HaplotypeScore=50.8133;MQ=60.00;MQ0=0;QD=1.90;SB=-48.80;VQSLOD=-1.9958;sumGLbyD=2.38	GT:AD:DP:GQ:PL	0/1:36,22:36:99:150,0,400
-20	25831452	.	A	G	36.28	PASS	AC=1;AF=0.50;AN=2;DP=55;Dels=0.00;HRun=2;HaplotypeScore=67.9389;MQ=60.00;MQ0=0;QD=0.66;SB=-12.31;VQSLOD=-4.0044;sumGLbyD=1.20	GT:AD:DP:GQ:PL	0/1:45,10:24:66.27:66,0,338
-20	25890781	.	C	T	193.11	PASS	AC=1;AF=0.50;AN=2;DP=63;Dels=0.11;HRun=2;HaplotypeScore=113.7832;MQ=60.00;MQ0=0;QD=3.07;SB=-107.12;VQSLOD=-2.2487;sumGLbyD=3.54	GT:AD:DP:GQ:PL	0/1:33,21:48:99:223,0,564
-20	25891018	.	G	A	34.89	PASS	AC=1;AF=0.50;AN=2;DP=78;Dels=0.10;HRun=0;HaplotypeScore=131.9142;MQ=60.00;MQ0=0;QD=0.45;SB=18.43;VQSLOD=-2.3685;sumGLbyD=0.83	GT:AD:DP:GQ:PL	0/1:57,9:53:64.89:65,0,833
-20	25891108	.	C	T	50.30	PASS	AC=1;AF=0.50;AN=2;DP=94;Dels=0.05;HRun=1;HaplotypeScore=97.3896;MQ=60.00;MQ0=0;QD=0.54;SB=-8.69;VQSLOD=-3.2126;sumGLbyD=0.85	GT:AD:DP:GQ:PL	0/1:73,15:74:80.29:80,0,1011
-20	25891206	rs6050983	G	A	567.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=103;Dels=0.10;HRun=1;HaplotypeScore=209.4534;MQ=60.00;MQ0=0;QD=5.51;SB=-272.67;VQSLOD=-1.6399;sumGLbyD=5.80	GT:AD:DP:GQ:PL	0/1:44,42:75:99:597,0,599
-20	25891232	.	C	T	39.79	PASS	AC=1;AF=0.50;AN=2;DP=105;Dels=0.09;HRun=2;HaplotypeScore=188.3148;MQ=60.00;MQ0=0;QD=0.38;SB=-5.12;VQSLOD=-3.2082;sumGLbyD=0.66	GT:AD:DP:GQ:PL	0/1:79,15:73:69.78:70,0,975
-20	25891252	rs6050984	C	T	77.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.25;HRun=0;HaplotypeScore=440.0378;MQ=60.00;MQ0=0;QD=0.73;SB=-9.26;VQSLOD=-2.6785;sumGLbyD=1.01	GT:AD:DP:GQ:PL	0/1:56,17:56:99:107,0,774
-20	25891391	.	G	A	44.71	PASS	AC=1;AF=0.50;AN=2;DP=147;Dels=0.03;HRun=0;HaplotypeScore=215.5627;MQ=60.00;MQ0=0;QD=0.30;SB=-14.54;VQSLOD=-1.7765;sumGLbyD=0.51	GT:AD:DP:GQ:PL	0/1:116,22:113:74.70:75,0,1901
-20	25891551	.	C	T	58.49	PASS	AC=1;AF=0.50;AN=2;DP=140;Dels=0.00;HRun=0;HaplotypeScore=92.4805;MQ=60.00;MQ0=0;QD=0.42;SB=-27.70;VQSLOD=-2.5935;sumGLbyD=0.63	GT:AD:DP:GQ:PL	0/1:118,20:85:88.49:88,0,1378
-20	25891567	.	G	A	86.30	PASS	AC=1;AF=0.50;AN=2;DP=137;Dels=0.00;HRun=1;HaplotypeScore=97.4280;MQ=60.00;MQ0=0;QD=0.63;SB=-16.70;VQSLOD=-3.0970;sumGLbyD=0.85	GT:AD:DP:GQ:PL	0/1:112,24:81:99:116,0,1248
-20	25891590	.	G	C	77.15	PASS	AC=1;AF=0.50;AN=2;DP=135;Dels=0.04;HRun=0;HaplotypeScore=172.1613;MQ=60.00;MQ0=0;QD=0.57;SB=-23.20;VQSLOD=-1.8427;sumGLbyD=0.79	GT:AD:DP:GQ:PL	0/1:103,25:94:99:107,0,1557
-20	25904917	rs6076395	G	T	46.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.00;HRun=0;HaplotypeScore=42.5903;MQ=60.00;MQ0=0;QD=1.10;SB=-35.20;VQSLOD=-2.7958;sumGLbyD=1.81	GT:AD:DP:GQ:PL	0/1:34,7:30:76.09:76,0,442
-20	25905264	rs13036925	T	C	255.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=81;Dels=0.07;HRun=0;HaplotypeScore=124.0633;MQ=60.00;MQ0=0;QD=3.16;SB=-139.61;VQSLOD=-0.3609;sumGLbyD=3.53	GT:AD:DP:GQ:PL	0/1:53,21:55:99:286,0,615
-20	26130942	.	G	C	92.07	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.00;HRun=0;HaplotypeScore=25.2725;MQ=60.00;MQ0=0;QD=1.62;SB=-27.82;VQSLOD=-2.6937;sumGLbyD=2.14	GT:AD:DP:GQ:PL	0/1:46,11:48:99:122,0,704
-20	26131001	.	T	A	57.60	PASS	AC=1;AF=0.50;AN=2;DP=62;Dels=0.11;HRun=1;HaplotypeScore=129.0072;MQ=60.00;MQ0=0;QD=0.93;SB=-23.24;VQSLOD=-2.6764;sumGLbyD=1.41	GT:AD:DP:GQ:PL	0/1:44,11:47:87.59:88,0,680
-20	26131123	.	G	A	82.31	PASS	AC=1;AF=0.50;AN=2;DP=70;Dels=0.01;HRun=0;HaplotypeScore=103.3413;MQ=60.00;MQ0=0;QD=1.18;SB=-3.32;VQSLOD=-2.2073;sumGLbyD=1.60	GT:AD:DP:GQ:PL	0/1:49,16:53:99:112,0,696
-20	26131133	.	A	G	94.82	PASS	AC=1;AF=0.50;AN=2;DP=70;Dels=0.04;HRun=0;HaplotypeScore=92.8547;MQ=60.00;MQ0=0;QD=1.35;SB=-53.88;VQSLOD=-1.8750;sumGLbyD=1.78	GT:AD:DP:GQ:PL	0/1:48,18:52:99:125,0,792
-20	26131210	rs2697510	G	A	263.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=83;Dels=0.19;HRun=0;HaplotypeScore=331.6569;MQ=60.00;MQ0=0;QD=3.18;SB=-118.08;VQSLOD=-1.3246;sumGLbyD=3.54	GT:AD:DP:GQ:PL	0/1:39,23:45:99:294,0,408
-20	26131303	.	T	C	144.15	PASS	AC=1;AF=0.50;AN=2;DP=100;Dels=0.03;HRun=0;HaplotypeScore=135.4056;MQ=60.00;MQ0=0;QD=1.44;SB=-23.56;VQSLOD=-1.6445;sumGLbyD=1.74	GT:AD:DP:GQ:PL	0/1:69,27:78:99:174,0,1231
-20	26131318	.	C	A	141.43	PASS	AC=1;AF=0.50;AN=2;DP=104;Dels=0.04;HRun=0;HaplotypeScore=152.4266;MQ=60.00;MQ0=0;QD=1.36;SB=-71.90;VQSLOD=-1.2884;sumGLbyD=1.65	GT:AD:DP:GQ:PL	0/1:70,24:68:99:171,0,990
-20	26131325	.	C	T	32.68	PASS	AC=1;AF=0.50;AN=2;DP=105;Dels=0.11;HRun=1;HaplotypeScore=216.0125;MQ=60.00;MQ0=0;QD=0.31;SB=-25.69;VQSLOD=-2.7139;sumGLbyD=0.60	GT:AD:DP:GQ:PL	0/1:75,14:74:62.67:63,0,1280
-20	26131360	.	A	C	216.86	PASS	AC=1;AF=0.50;AN=2;DP=117;Dels=0.09;HRun=1;HaplotypeScore=154.0256;MQ=60.00;MQ0=0;QD=1.85;SB=-121.78;VQSLOD=-1.6445;sumGLbyD=2.11	GT:AD:DP:GQ:PL	0/1:77,26:85:99:247,0,1276
-20	26131371	.	A	G	113.39	PASS	AC=1;AF=0.50;AN=2;DP=118;Dels=0.00;HRun=0;HaplotypeScore=77.2858;MQ=60.00;MQ0=0;QD=0.96;SB=-55.78;VQSLOD=-2.3457;sumGLbyD=1.22	GT:AD:DP:GQ:PL	0/1:82,27:82:99:143,0,1205
-20	26131434	.	C	T	444.72	PASS	AC=1;AF=0.50;AN=2;DP=124;Dels=0.01;HRun=2;HaplotypeScore=101.2635;MQ=60.00;MQ0=0;QD=3.59;SB=-175.53;VQSLOD=-2.1289;sumGLbyD=3.83	GT:AD:DP:GQ:PL	0/1:82,40:85:99:475,0,1025
-20	26131467	.	A	G	124.45	PASS	AC=1;AF=0.50;AN=2;DP=135;Dels=0.10;HRun=1;HaplotypeScore=272.5757;MQ=60.00;MQ0=0;QD=0.92;SB=-18.65;VQSLOD=-2.4790;sumGLbyD=1.14	GT:AD:DP:GQ:PL	0/1:92,26:89:99:154,0,1406
-20	26131562	.	T	C	310.14	PASS	AC=1;AF=0.50;AN=2;DP=144;Dels=0.06;HRun=0;HaplotypeScore=273.3457;MQ=60.00;MQ0=0;QD=2.15;SB=-102.51;VQSLOD=-0.8407;sumGLbyD=2.36	GT:AD:DP:GQ:PL	0/1:88,43:94:99:340,0,1280
-20	26131603	.	C	G	285.99	PASS	AC=1;AF=0.50;AN=2;DP=145;Dels=0.18;HRun=0;HaplotypeScore=411.0003;MQ=60.00;MQ0=0;QD=1.97;SB=-116.55;VQSLOD=-1.2098;sumGLbyD=2.18	GT:AD:DP:GQ:PL	0/1:82,32:77:99:316,0,891
-20	26131681	.	T	A	160.04	PASS	AC=1;AF=0.50;AN=2;DP=129;Dels=0.02;HRun=0;HaplotypeScore=119.7802;MQ=60.00;MQ0=0;QD=1.24;SB=-93.78;VQSLOD=-1.5421;sumGLbyD=1.47	GT:AD:DP:GQ:PL	0/1:89,37:79:99:190,0,1197
-20	26131714	.	A	G	42.71	PASS	AC=1;AF=0.50;AN=2;DP=115;Dels=0.00;HRun=0;HaplotypeScore=88.6711;MQ=60.00;MQ0=0;QD=0.37;SB=0.84;VQSLOD=-2.7593;sumGLbyD=0.63	GT:AD:DP:GQ:PL	0/1:95,18:57:72.71:73,0,885
-20	26131744	.	C	G	127.59	PASS	AC=1;AF=0.50;AN=2;DP=103;Dels=0.01;HRun=0;HaplotypeScore=84.1409;MQ=60.00;MQ0=0;QD=1.24;SB=-70.64;VQSLOD=-1.9834;sumGLbyD=1.53	GT:AD:DP:GQ:PL	0/1:76,24:62:99:158,0,833
-20	26131748	.	T	C	88.77	PASS	AC=1;AF=0.50;AN=2;DP=103;Dels=0.08;HRun=0;HaplotypeScore=180.3277;MQ=60.00;MQ0=0;QD=0.86;SB=-37.87;VQSLOD=-1.6056;sumGLbyD=1.15	GT:AD:DP:GQ:PL	0/1:69,24:55:99:119,0,810
-20	26131755	.	G	A	214.77	PASS	AC=1;AF=0.50;AN=2;DP=101;Dels=0.06;HRun=0;HaplotypeScore=167.7765;MQ=60.00;MQ0=0;QD=2.13;SB=-120.57;VQSLOD=-0.5760;sumGLbyD=2.42	GT:AD:DP:GQ:PL	0/1:69,23:61:99:245,0,825
-20	26131777	.	T	C	80.43	PASS	AC=1;AF=0.50;AN=2;DP=92;Dels=0.08;HRun=0;HaplotypeScore=152.2912;MQ=60.00;MQ0=0;QD=0.87;SB=-36.93;VQSLOD=-1.7622;sumGLbyD=1.20	GT:AD:DP:GQ:PL	0/1:69,15:44:99:110,0,609
-20	26131803	.	C	A	179.62	PASS	AC=1;AF=0.50;AN=2;DP=85;Dels=0.04;HRun=0;HaplotypeScore=81.5051;MQ=60.00;MQ0=0;QD=2.11;SB=-85.98;VQSLOD=-1.2887;sumGLbyD=2.47	GT:AD:DP:GQ:PL	0/1:55,24:50:99:210,0,692
-20	26131872	.	A	G	33.79	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.02;HRun=0;HaplotypeScore=38.3012;MQ=60.00;MQ0=0;QD=0.66;SB=2.56;VQSLOD=-3.3273;sumGLbyD=1.25	GT:AD:DP:GQ:PL	0/1:34,11:38:63.78:64,0,524
-20	26131879	.	T	C	87.62	PASS	AC=1;AF=0.50;AN=2;DP=50;Dels=0.02;HRun=0;HaplotypeScore=39.1091;MQ=60.00;MQ0=0;QD=1.75;SB=-29.20;VQSLOD=-2.3968;sumGLbyD=2.35	GT:AD:DP:GQ:PL	0/1:37,11:33:99:118,0,452
-20	26131880	.	G	A	90.78	PASS	AC=1;AF=0.50;AN=2;DP=49;Dels=0.04;HRun=0;HaplotypeScore=48.0151;MQ=60.00;MQ0=0;QD=1.85;SB=-32.34;VQSLOD=-2.1860;sumGLbyD=2.46	GT:AD:DP:GQ:PL	0/1:34,12:34:99:121,0,434
-20	26132070	.	A	G	56.36	PASS	AC=1;AF=0.50;AN=2;DP=25;Dels=0.00;HRun=0;HaplotypeScore=18.9358;MQ=60.00;MQ0=0;QD=2.25;SB=5.98;VQSLOD=-2.7118;sumGLbyD=3.45	GT:AD:DP:GQ:PL	0/1:16,9:18:86.36:86,0,213
-20	26132071	.	C	T	31.71	PASS	AC=1;AF=0.50;AN=2;DP=25;Dels=0.08;HRun=1;HaplotypeScore=38.0276;MQ=60.00;MQ0=0;QD=1.27;SB=5.92;VQSLOD=-3.5718;sumGLbyD=2.47	GT:AD:DP:GQ:PL	0/1:14,8:17:61.70:62,0,210
-20	26132130	.	C	T	55.55	PASS	AC=1;AF=0.50;AN=2;DP=26;Dels=0.00;HRun=0;HaplotypeScore=18.8540;MQ=60.00;MQ0=0;QD=2.14;SB=-32.67;VQSLOD=-2.3942;sumGLbyD=3.29	GT:AD:DP:GQ:PL	0/1:18,7:19:85.54:86,0,222
-20	26132150	.	A	G	47.54	PASS	AC=1;AF=0.50;AN=2;DP=24;Dels=0.04;HRun=0;HaplotypeScore=26.3205;MQ=60.00;MQ0=0;QD=1.98;SB=-13.71;VQSLOD=-2.5540;sumGLbyD=3.23	GT:AD:DP:GQ:PL	0/1:12,10:15:77.53:78,0,169
-20	26132190	.	A	G	61.21	PASS	AC=1;AF=0.50;AN=2;DP=21;Dels=0.00;HRun=1;HaplotypeScore=21.6525;MQ=60.00;MQ0=0;QD=2.91;SB=-36.39;VQSLOD=-3.0814;sumGLbyD=4.34	GT:AD:DP:GQ:PL	0/1:14,7:15:91.21:91,0,167
-20	26132403	.	T	C	42.47	PASS	AC=1;AF=0.50;AN=2;DP=59;Dels=0.00;HRun=0;HaplotypeScore=31.7449;MQ=60.00;MQ0=0;QD=0.72;SB=-8.15;VQSLOD=-3.3413;sumGLbyD=1.23	GT:AD:DP:GQ:PL	0/1:48,11:48:72.47:72,0,795
-20	26132507	.	C	A	65.16	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.10;HRun=0;HaplotypeScore=159.2829;MQ=60.00;MQ0=0;QD=0.89;SB=-10.07;VQSLOD=-1.8554;sumGLbyD=1.30	GT:AD:DP:GQ:PL	0/1:49,15:55:95.16:95,0,812
-20	26132607	.	T	C	61.95	PASS	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=58.2245;MQ=60.00;MQ0=0;QD=0.70;SB=-8.85;VQSLOD=-2.9656;sumGLbyD=1.04	GT:AD:DP:GQ:PL	0/1:72,14:65:91.94:92,0,1033
-20	26132662	.	T	A	42.78	PASS	AC=1;AF=0.50;AN=2;DP=102;Dels=0.06;HRun=2;HaplotypeScore=111.4160;MQ=60.00;MQ0=0;QD=0.42;SB=-34.92;VQSLOD=-3.5562;sumGLbyD=0.71	GT:AD:DP:GQ:PL	0/1:79,16:77:72.77:73,0,1226
-20	26132682	.	A	G	58.09	PASS	AC=1;AF=0.50;AN=2;DP=108;Dels=0.00;HRun=0;HaplotypeScore=86.4197;MQ=60.00;MQ0=0;QD=0.54;SB=-34.58;VQSLOD=-2.5827;sumGLbyD=0.82	GT:AD:DP:GQ:PL	0/1:91,17:74:88.09:88,0,1138
-20	26132732	.	G	A	86.58	PASS	AC=1;AF=0.50;AN=2;DP=110;Dels=0.01;HRun=0;HaplotypeScore=111.8568;MQ=60.00;MQ0=0;QD=0.79;SB=-13.82;VQSLOD=-2.2580;sumGLbyD=1.06	GT:AD:DP:GQ:PL	0/1:87,21:92:99:117,0,1389
-20	26132794	.	G	A	46.66	PASS	AC=1;AF=0.50;AN=2;DP=119;Dels=0.02;HRun=0;HaplotypeScore=85.6948;MQ=60.00;MQ0=0;QD=0.39;SB=-1.07;VQSLOD=-2.7800;sumGLbyD=0.64	GT:AD:DP:GQ:PL	0/1:96,18:97:76.66:77,0,1316
-20	26132816	rs2697509	G	T	608.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.15;HRun=4;HaplotypeScore=247.4357;MQ=60.00;MQ0=0;QD=4.95;SB=-310.83;VQSLOD=-6.7455;sumGLbyD=5.19	GT:AD:DP:GQ:PL	0/1:49,52:77:99:638,0,682
-20	26142569	rs6138815	C	T	288.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.00;HRun=1;HaplotypeScore=257.3762;MQ=60.00;MQ0=0;QD=2.15;SB=-147.82;VQSLOD=-1.3845;sumGLbyD=2.37	GT:AD:DP:GQ:PL	0/1:90,43:65:99:318,0,769
-20	26143056	.	A	G	816.68	PASS	AC=1;AF=0.50;AN=2;DP=188;DS;Dels=0.02;HRun=0;HaplotypeScore=234.7230;MQ=60.00;MQ0=0;QD=4.34;SB=-329.26;VQSLOD=-0.5083;sumGLbyD=4.50	GT:AD:DP:GQ:PL	0/1:97,74:135:99:847,0,1386
-20	26146115	rs845981	G	A	655.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=75;Dels=0.17;HRun=1;HaplotypeScore=229.9472;MQ=60.00;MQ0=0;QD=8.74;SB=-300.01;VQSLOD=-2.9250;sumGLbyD=9.15	GT:AD:DP:GQ:PL	0/1:14,45:39:2.81:684,0,3
-20	26146163	rs845982	C	T	571.49	PASS	AC=2;AF=1.00;AN=2;DB;DP=69;Dels=0.28;HRun=4;HaplotypeScore=232.2860;MQ=60.00;MQ0=0;QD=8.28;SB=-236.25;VQSLOD=-9.9530;sumGLbyD=8.76	GT:AD:DP:GQ:PL	1/1:1,45:28:77.70:604,78,0
-20	26148657	.	C	T	40.06	PASS	AC=1;AF=0.50;AN=2;DP=82;Dels=0.29;HRun=2;HaplotypeScore=341.8972;MQ=60.00;MQ0=0;QD=0.49;SB=3.48;VQSLOD=-3.1262;sumGLbyD=0.85	GT:AD:DP:GQ:PL	0/1:48,8:40:70.06:70,0,603
-20	26207410	rs62198215	T	C	408.42	PASS	AC=2;AF=1.00;AN=2;DB;DP=49;Dels=0.10;HRun=0;HaplotypeScore=100.8080;MQ=60.00;MQ0=0;QD=8.34;SB=-214.67;VQSLOD=-0.9324;sumGLbyD=9.01	GT:AD:DP:GQ:PL	1/1:5,37:27:32.48:441,32,0
-20	26207418	rs62198216	G	C	226.56	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.16;HRun=1;HaplotypeScore=164.7602;MQ=60.00;MQ0=0;QD=4.62;SB=-113.10;VQSLOD=-1.3394;sumGLbyD=5.24	GT:AD:DP:GQ:PL	0/1:12,25:21:59.68:257,0,60
-20	26207458	.	A	C	291.60	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=75.6204;MQ=60.00;MQ0=0;QD=5.40;SB=-100.99;VQSLOD=-1.4208;sumGLbyD=5.96	GT:AD:DP:GQ:PL	0/1:22,25:26:99:322,0,131
-20	26207460	.	C	T	197.33	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.07;HRun=1;HaplotypeScore=138.3704;MQ=60.00;MQ0=0;QD=3.65;SB=-73.79;VQSLOD=-1.8291;sumGLbyD=4.21	GT:AD:DP:GQ:PL	0/1:18,18:24:99:227,0,113
-20	26207461	.	A	G	187.39	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.04;HRun=0;HaplotypeScore=120.6189;MQ=60.00;MQ0=0;QD=3.47;SB=-93.49;VQSLOD=-0.6123;sumGLbyD=4.03	GT:AD:DP:GQ:PL	0/1:21,25:27:99:217,0,210
-20	26207469	.	G	C	477.97	PASS	AC=1;AF=0.50;AN=2;DP=54;Dels=0.00;HRun=0;HaplotypeScore=100.6899;MQ=60.00;MQ0=0;QD=8.85;SB=-184.93;VQSLOD=-1.3647;sumGLbyD=9.41	GT:AD:DP:GQ:PL	0/1:22,31:36:99:508,0,123
-20	26207492	rs1818576	G	T	42.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.09;HRun=1;HaplotypeScore=126.1470;MQ=60.00;MQ0=0;QD=0.75;SB=-29.91;VQSLOD=-2.7349;sumGLbyD=1.27	GT:AD:DP:GQ:PL	0/1:44,8:38:72.57:73,0,497
-20	26207505	.	G	T	404.10	PASS	AC=1;AF=0.50;AN=2;DP=57;Dels=0.21;HRun=1;HaplotypeScore=192.7340;MQ=60.00;MQ0=0;QD=7.09;SB=-215.48;VQSLOD=-1.3268;sumGLbyD=7.62	GT:AD:DP:GQ:PL	0/1:19,26:37:99:434,0,205
-20	26207516	.	T	G	269.05	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.00;HRun=0;HaplotypeScore=76.1208;MQ=60.00;MQ0=0;QD=4.64;SB=-74.72;VQSLOD=-1.3362;sumGLbyD=5.16	GT:AD:DP:GQ:PL	0/1:33,25:22:69.33:299,0,69
-20	26207518	.	C	A	391.23	PASS	AC=1;AF=0.50;AN=2;DP=58;Dels=0.12;HRun=0;HaplotypeScore=131.6809;MQ=60.00;MQ0=0;QD=6.75;SB=-128.80;VQSLOD=-1.1307;sumGLbyD=7.26	GT:AD:DP:GQ:PL	0/1:17,29:34:99:421,0,157
-20	26207612	rs62198217	C	A	419.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=70;Dels=0.03;HRun=0;HaplotypeScore=104.0998;MQ=60.00;MQ0=0;QD=6.00;SB=-173.12;VQSLOD=-1.0615;sumGLbyD=6.43	GT:AD:DP:GQ:PL	0/1:17,45:36:99:450,0,137
-20	26207673	rs62198218	G	A	802.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.09;HRun=0;HaplotypeScore=156.8217;MQ=60.00;MQ0=0;QD=10.03;SB=-381.14;VQSLOD=-2.7898;sumGLbyD=10.40	GT:AD:DP:GQ:PL	0/1:21,50:53:99:832,0,122
-20	26207726	rs62198219	T	C	926.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=97;Dels=0.05;HRun=0;HaplotypeScore=183.4907;MQ=60.00;MQ0=0;QD=9.55;SB=-347.26;VQSLOD=-2.7577;sumGLbyD=9.86	GT:AD:DP:GQ:PL	0/1:29,61:66:99:956,0,164
-20	26207735	rs62198220	T	C	847.58	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;Dels=0.09;HRun=0;HaplotypeScore=235.1710;MQ=60.00;MQ0=0;QD=8.48;SB=-426.05;VQSLOD=-1.7066;sumGLbyD=8.78	GT:AD:DP:GQ:PL	0/1:27,61:64:99:878,0,206
-20	26207749	.	T	C	768.97	PASS	AC=1;AF=0.50;AN=2;DP=105;Dels=0.05;HRun=0;HaplotypeScore=134.0146;MQ=60.00;MQ0=0;QD=7.32;SB=-386.13;VQSLOD=-1.4259;sumGLbyD=7.61	GT:AD:DP:GQ:PL	0/1:41,54:72:99:799,0,383
-20	26207779	.	G	A	979.52	PASS	AC=1;AF=0.50;AN=2;DP=108;Dels=0.06;HRun=0;HaplotypeScore=168.2152;MQ=60.00;MQ0=0;QD=9.07;SB=-394.12;VQSLOD=-2.0333;sumGLbyD=9.35	GT:AD:DP:GQ:PL	0/1:27,68:70:99:1010,0,219
-20	26207820	rs62198221	C	T	1169.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=121;Dels=0.07;HRun=1;HaplotypeScore=272.4883;MQ=60.00;MQ0=0;QD=9.67;SB=-442.74;VQSLOD=-2.4281;sumGLbyD=9.91	GT:AD:DP:GQ:PL	0/1:37,68:85:99:1200,0,131
-20	26207823	rs62198222	G	A	991.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=121;Dels=0.21;HRun=1;HaplotypeScore=469.2784;MQ=60.00;MQ0=0;QD=8.19;SB=-458.77;VQSLOD=-2.5289;sumGLbyD=8.44	GT:AD:DP:GQ:PL	0/1:38,57:75:99:1021,0,281
-20	26207888	rs62198223	T	C	829.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=153;Dels=0.21;HRun=0;HaplotypeScore=465.2394;MQ=60.00;MQ0=0;QD=5.42;SB=-380.21;VQSLOD=-1.6930;sumGLbyD=5.62	GT:AD:DP:GQ:PL	0/1:27,74:66:99:860,0,208
-20	26207905	rs2380063	T	G	240.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=152;Dels=0.05;HRun=0;HaplotypeScore=240.5927;MQ=60.00;MQ0=0;QD=1.58;SB=-111.56;VQSLOD=-0.8429;sumGLbyD=1.78	GT:AD:DP:GQ:PL	0/1:106,37:79:99:270,0,1093
-20	26207929	rs2946020	T	C	76.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=153;Dels=0.11;HRun=2;HaplotypeScore=322.3803;MQ=60.00;MQ0=0;QD=0.50;SB=-38.25;VQSLOD=-2.8356;sumGLbyD=0.70	GT:AD:DP:GQ:PL	0/1:108,25:100:99:106,0,1621
-20	26207975	.	T	C	1009.54	PASS	AC=1;AF=0.50;AN=2;DP=160;Dels=0.18;HRun=1;HaplotypeScore=548.6023;MQ=60.00;MQ0=0;QD=6.31;SB=-505.03;VQSLOD=-3.8476;sumGLbyD=6.50	GT:AD:DP:GQ:PL	0/1:60,65:98:99:1040,0,659
-20	26208019	.	T	C	864.22	PASS	AC=1;AF=0.50;AN=2;DP=162;Dels=0.20;HRun=1;HaplotypeScore=566.8822;MQ=60.00;MQ0=0;QD=5.33;SB=-344.57;VQSLOD=-2.5483;sumGLbyD=5.52	GT:AD:DP:GQ:PL	0/1:63,61:93:99:894,0,714
-20	26208024	.	C	T	1277.75	PASS	AC=1;AF=0.50;AN=2;DP=162;Dels=0.06;HRun=0;HaplotypeScore=352.1320;MQ=60.00;MQ0=0;QD=7.89;SB=-634.68;VQSLOD=-2.7244;sumGLbyD=8.07	GT:AD:DP:GQ:PL	0/1:52,98:112:99:1308,0,619
-20	26208032	.	C	A	1208.56	PASS	AC=1;AF=0.50;AN=2;DP=162;Dels=0.04;HRun=0;HaplotypeScore=258.0450;MQ=60.00;MQ0=0;QD=7.46;SB=-607.15;VQSLOD=-1.9560;sumGLbyD=7.65	GT:AD:DP:GQ:PL	0/1:56,91:111:99:1239,0,583
-20	26208052	.	G	A	1273.30	PASS	AC=1;AF=0.50;AN=2;DP=166;Dels=0.13;HRun=2;HaplotypeScore=365.6795;MQ=60.00;MQ0=0;QD=7.67;SB=-641.33;VQSLOD=-5.5102;sumGLbyD=7.85	GT:AD:DP:GQ:PL	0/1:45,85:107:99:1303,0,468
-20	26208072	.	A	T	1025.84	PASS	AC=1;AF=0.50;AN=2;DP=170;Dels=0.00;HRun=0;HaplotypeScore=108.6585;MQ=60.00;MQ0=0;QD=6.03;SB=-478.97;VQSLOD=-1.6736;sumGLbyD=6.21	GT:AD:DP:GQ:PL	0/1:95,72:111:99:1056,0,847
-20	26208102	rs62198224	T	C	1464.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.05;HRun=0;HaplotypeScore=255.9076;MQ=60.00;MQ0=0;QD=8.66;SB=-668.44;VQSLOD=-2.1550;sumGLbyD=8.84	GT:AD:DP:GQ:PL	0/1:39,105:108:99:1494,0,364
-20	26208156	.	T	C	486.57	PASS	AC=1;AF=0.50;AN=2;DP=163;Dels=0.36;HRun=4;HaplotypeScore=902.2959;MQ=60.00;MQ0=0;QD=2.99;SB=-241.44;VQSLOD=-4.4928;sumGLbyD=3.17	GT:AD:DP:GQ:PL	0/1:39,52:67:99:517,0,557
-20	26208169	rs4009838	G	C	473.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.12;HRun=2;HaplotypeScore=380.3144;MQ=60.00;MQ0=0;QD=2.98;SB=-225.52;VQSLOD=-2.1007;sumGLbyD=3.17	GT:AD:DP:GQ:PL	0/1:77,53:82:99:504,0,822
-20	26208179	.	A	C	1522.40	PASS	AC=1;AF=0.50;AN=2;DP=157;Dels=0.03;HRun=0;HaplotypeScore=199.8099;MQ=60.00;MQ0=0;QD=9.70;SB=-744.95;VQSLOD=-2.3614;sumGLbyD=9.89	GT:AD:DP:GQ:PL	0/1:53,96:111:99:1552,0,393
-20	26208255	.	C	T	1246.64	PASS	AC=1;AF=0.50;AN=2;DP=143;Dels=0.06;HRun=1;HaplotypeScore=173.9702;MQ=60.00;MQ0=0;QD=8.72;SB=-606.19;VQSLOD=-3.7283;sumGLbyD=8.93	GT:AD:DP:GQ:PL	0/1:36,96:85:99:1277,0,151
-20	26208280	rs62198225	T	C	1092.67	PASS	AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.03;HRun=0;HaplotypeScore=142.4898;MQ=60.00;MQ0=0;QD=8.88;SB=-533.81;VQSLOD=-1.5381;sumGLbyD=9.13	GT:AD:DP:GQ:PL	0/1:24,91:77:99:1123,0,205
-20	26208328	.	T	C	755.49	PASS	AC=1;AF=0.50;AN=2;DP=110;Dels=0.00;HRun=0;HaplotypeScore=116.4057;MQ=60.00;MQ0=0;QD=6.87;SB=-302.18;VQSLOD=-1.6010;sumGLbyD=7.14	GT:AD:DP:GQ:PL	0/1:44,64:65:99:785,0,364
-20	26208334	.	C	T	1159.39	PASS	AC=1;AF=0.50;AN=2;DP=108;Dels=0.01;HRun=0;HaplotypeScore=148.1987;MQ=60.00;MQ0=0;QD=10.74;SB=-439.30;VQSLOD=-2.8104;sumGLbyD=11.01	GT:AD:DP:GQ:PL	0/1:27,74:81:99:1189,0,246
-20	26208375	.	T	C	762.39	PASS	AC=1;AF=0.50;AN=2;DP=103;Dels=0.00;HRun=0;HaplotypeScore=66.8726;MQ=60.00;MQ0=0;QD=7.40;SB=-331.89;VQSLOD=-1.9967;sumGLbyD=7.69	GT:AD:DP:GQ:PL	0/1:41,62:61:99:792,0,271
-20	26208430	.	T	C	645.66	PASS	AC=1;AF=0.50;AN=2;DP=91;Dels=0.18;HRun=1;HaplotypeScore=241.7358;MQ=60.00;MQ0=0;QD=7.10;SB=-281.79;VQSLOD=-2.3403;sumGLbyD=7.42	GT:AD:DP:GQ:PL	0/1:25,46:54:99:676,0,223
-20	26208454	.	A	G	410.45	PASS	AC=1;AF=0.50;AN=2;DP=85;Dels=0.25;HRun=0;HaplotypeScore=384.4188;MQ=60.00;MQ0=0;QD=4.83;SB=-177.90;VQSLOD=-2.3749;sumGLbyD=5.18	GT:AD:DP:GQ:PL	0/1:12,44:42:99:440,0,115
-20	26208455	.	C	T	451.67	PASS	AC=1;AF=0.50;AN=2;DP=85;Dels=0.01;HRun=0;HaplotypeScore=132.5480;MQ=60.00;MQ0=0;QD=5.31;SB=-92.62;VQSLOD=-1.3591;sumGLbyD=5.67	GT:AD:DP:GQ:PL	0/1:36,41:47:99:482,0,230
-20	26208477	.	T	G	641.20	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.12;HRun=1;HaplotypeScore=192.1126;MQ=60.00;MQ0=0;QD=7.92;SB=-239.33;VQSLOD=-1.7707;sumGLbyD=8.29	GT:AD:DP:GQ:PL	0/1:17,45:50:99:671,0,100
-20	26208508	rs62198226	T	C	605.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=74;Dels=0.04;HRun=0;HaplotypeScore=107.1924;MQ=60.00;MQ0=0;QD=8.18;SB=-250.20;VQSLOD=-1.5910;sumGLbyD=8.59	GT:AD:DP:GQ:PL	0/1:13,51:41:64.97:636,0,65
-20	26208600	rs62198227	C	T	343.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=60;Dels=0.00;HRun=0;HaplotypeScore=66.1409;MQ=60.00;MQ0=0;QD=5.72;SB=-97.48;VQSLOD=-1.5565;sumGLbyD=6.22	GT:AD:DP:GQ:PL	0/1:32,26:36:99:373,0,248
-20	26208691	rs2889440	C	T	389.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.02;HRun=0;HaplotypeScore=54.7358;MQ=60.00;MQ0=0;QD=6.83;SB=-114.18;VQSLOD=-1.3768;sumGLbyD=7.36	GT:AD:DP:GQ:PL	0/1:17,38:30:99:420,0,116
-20	26208762	rs62198229	C	T	289.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.16;HRun=1;HaplotypeScore=115.1333;MQ=60.00;MQ0=0;QD=6.74;SB=-59.14;VQSLOD=-1.9872;sumGLbyD=7.44	GT:AD:DP:GQ:PL	0/1:9,26:25:79.89:320,0,80
-20	26208776	rs62198231	C	T	119.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.00;HRun=0;HaplotypeScore=24.9583;MQ=60.00;MQ0=0;QD=3.00;SB=3.02;VQSLOD=-2.3432;sumGLbyD=3.75	GT:AD:DP:GQ:PL	0/1:14,25:10:40.07:150,0,40
-20	26208792	rs4085457	C	G	47.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=36;Dels=0.22;HRun=1;HaplotypeScore=91.8418;MQ=60.00;MQ0=0;QD=1.32;SB=5.98;VQSLOD=-3.0371;sumGLbyD=2.15	GT:AD:DP:GQ:PL	0/1:10,15:12:77.52:78,0,126
-20	26210767	.	C	T	699.30	PASS	AC=1;AF=0.50;AN=2;DP=220;Dels=0.00;HRun=1;HaplotypeScore=196.2080;MQ=60.00;MQ0=0;QD=3.18;SB=-288.07;VQSLOD=-1.3616;sumGLbyD=3.31	GT:AD:DP:GQ:PL	0/1:139,77:130:99:729,0,1473
-20	29420590	rs7346438	C	T	172.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.05;HRun=0;HaplotypeScore=133.5925;MQ=60.00;MQ0=0;QD=2.03;SB=-69.48;VQSLOD=-1.0114;sumGLbyD=2.39	GT:AD:DP:GQ:PL	0/1:62,18:69:99:203,0,831
-20	29420606	rs7346440	C	A	253.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.01;HRun=0;HaplotypeScore=85.6550;MQ=60.00;MQ0=0;QD=2.98;SB=-41.44;VQSLOD=-1.2486;sumGLbyD=3.34	GT:AD:DP:GQ:PL	0/1:53,29:62:99:284,0,688
-20	29420618	.	T	A	85.86	PASS	AC=1;AF=0.50;AN=2;DP=87;Dels=0.22;HRun=2;HaplotypeScore=327.2635;MQ=60.00;MQ0=0;QD=0.99;SB=10.51;VQSLOD=-2.8865;sumGLbyD=1.33	GT:AD:DP:GQ:PL	0/1:44,22:49:99:116,0,722
-20	29420622	rs7348822	T	C	243.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.00;HRun=0;HaplotypeScore=130.7354;MQ=60.00;MQ0=0;QD=2.80;SB=-27.90;VQSLOD=-1.1663;sumGLbyD=3.15	GT:AD:DP:GQ:PL	0/1:48,31:55:99:274,0,691
-20	29420637	rs7345505	A	G	438.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=92;Dels=0.12;HRun=1;HaplotypeScore=222.6860;MQ=60.00;MQ0=0;QD=4.77;SB=-186.65;VQSLOD=-1.1261;sumGLbyD=5.09	GT:AD:DP:GQ:PL	0/1:49,31:73:99:469,0,843
-20	29420761	rs7348839	T	A	380.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=110;Dels=0.00;HRun=2;HaplotypeScore=86.7545;MQ=60.00;MQ0=0;QD=3.46;SB=-91.78;VQSLOD=-2.5998;sumGLbyD=3.73	GT:AD:DP:GQ:PL	0/1:64,41:68:99:410,0,731
-20	29420854	rs7346487	C	A	792.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=138;Dels=0.06;HRun=1;HaplotypeScore=188.3287;MQ=60.00;MQ0=0;QD=5.75;SB=-318.63;VQSLOD=-1.9830;sumGLbyD=5.96	GT:AD:DP:GQ:PL	0/1:62,65:98:99:823,0,882
-20	29420980	.	C	G	159.34	PASS	AC=1;AF=0.50;AN=2;DP=212;Dels=0.06;HRun=1;HaplotypeScore=270.5040;MQ=60.00;MQ0=0;QD=0.75;SB=-5.79;VQSLOD=-2.6480;sumGLbyD=0.89	GT:AD:DP:GQ:PL	0/1:157,31:167:99:189,0,2667
-20	29421068	rs62199548	T	A	755.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=250;DS;Dels=0.04;HRun=2;HaplotypeScore=297.0561;MQ=60.00;MQ0=0;QD=3.02;SB=-339.64;VQSLOD=-2.2633;sumGLbyD=3.14	GT:AD:DP:GQ:PL	0/1:147,87:187:99:785,0,2437
-20	29421079	rs62199549	T	C	225.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=248;DS;Dels=0.08;HRun=1;HaplotypeScore=373.6703;MQ=60.00;MQ0=0;QD=0.91;SB=-113.72;VQSLOD=-1.8338;sumGLbyD=1.03	GT:AD:DP:GQ:PL	0/1:182,40:174:99:255,0,2726
-20	29421159	.	G	A	1014.47	PASS	AC=1;AF=0.50;AN=2;DP=249;DS;Dels=0.10;HRun=0;HaplotypeScore=559.8247;MQ=60.00;MQ0=0;QD=4.07;SB=-469.01;VQSLOD=-1.4100;sumGLbyD=4.19	GT:AD:DP:GQ:PL	0/1:138,81:158:99:1044,0,1389
-20	29421162	.	C	A	709.61	PASS	AC=1;AF=0.50;AN=2;DP=248;DS;Dels=0.00;HRun=0;HaplotypeScore=246.6138;MQ=60.00;MQ0=0;QD=2.86;SB=-278.75;VQSLOD=-0.4150;sumGLbyD=2.98	GT:AD:DP:GQ:PL	0/1:172,73:136:99:740,0,1457
-20	29421199	rs11906444	A	C	919.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=248;DS;Dels=0.00;HRun=0;HaplotypeScore=250.7637;MQ=60.00;MQ0=0;QD=3.71;SB=-438.55;VQSLOD=-0.5917;sumGLbyD=3.83	GT:AD:DP:GQ:PL	0/1:134,97:159:99:950,0,1457
-20	29421209	rs35184392	C	T	138.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=250;DS;Dels=0.24;HRun=0;HaplotypeScore=1017.7237;MQ=60.00;MQ0=0;QD=0.55;SB=-83.25;VQSLOD=-5.2141;sumGLbyD=0.67	GT:AD:DP:GQ:PL	0/1:144,34:126:99:168,0,1805
-20	29421211	.	C	T	72.63	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.00;HRun=0;HaplotypeScore=216.4261;MQ=60.00;MQ0=0;QD=0.29;SB=-45.54;VQSLOD=-1.6932;sumGLbyD=0.41	GT:AD:DP:GQ:PL	0/1:210,34:137:99:103,0,2223
-20	29421255	.	T	A	1125.30	PASS	AC=1;AF=0.50;AN=2;DP=249;DS;Dels=0.04;HRun=0;HaplotypeScore=329.3808;MQ=60.00;MQ0=0;QD=4.52;SB=-472.01;VQSLOD=-0.5739;sumGLbyD=4.64	GT:AD:DP:GQ:PL	0/1:132,97:153:99:1155,0,1461
-20	29421258	.	C	T	1382.27	PASS	AC=1;AF=0.50;AN=2;DP=249;DS;Dels=0.13;HRun=2;HaplotypeScore=601.2714;MQ=60.00;MQ0=0;QD=5.55;SB=-649.10;VQSLOD=-5.0671;sumGLbyD=5.67	GT:AD:DP:GQ:PL	0/1:95,112:165:99:1412,0,1254
-20	29421304	.	A	T	929.98	PASS	AC=1;AF=0.50;AN=2;DP=246;DS;Dels=0.02;HRun=0;HaplotypeScore=236.1089;MQ=60.00;MQ0=0;QD=3.78;SB=-407.95;VQSLOD=-0.4981;sumGLbyD=3.90	GT:AD:DP:GQ:PL	0/1:161,73:184:99:960,0,2378
-20	29421338	rs6118902	A	T	1862.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=242;DS;Dels=0.03;HRun=0;HaplotypeScore=310.6997;MQ=60.00;MQ0=0;QD=7.70;SB=-925.95;VQSLOD=-3.1589;sumGLbyD=7.82	GT:AD:DP:GQ:PL	0/1:99,125:174:99:1892,0,1130
-20	29421350	rs8119325	A	G	454.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=247;DS;Dels=0.05;HRun=0;HaplotypeScore=454.9869;MQ=60.00;MQ0=0;QD=1.84;SB=-214.81;VQSLOD=-1.0713;sumGLbyD=1.96	GT:AD:DP:GQ:PL	0/1:166,63:162:99:484,0,2126
-20	29421362	.	C	G	485.11	PASS	AC=1;AF=0.50;AN=2;DP=244;DS;Dels=0.00;HRun=0;HaplotypeScore=248.9354;MQ=60.00;MQ0=0;QD=1.99;SB=-138.07;VQSLOD=-0.6139;sumGLbyD=2.11	GT:AD:DP:GQ:PL	0/1:168,66:161:99:515,0,2114
-20	29421423	.	T	A	602.81	PASS	AC=1;AF=0.50;AN=2;DP=232;DS;Dels=0.03;HRun=1;HaplotypeScore=287.7069;MQ=60.00;MQ0=0;QD=2.60;SB=-296.98;VQSLOD=-1.7167;sumGLbyD=2.73	GT:AD:DP:GQ:PL	0/1:155,61:155:99:633,0,2030
-20	29421504	rs62199551	G	C	397.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=186;DS;Dels=0.31;HRun=2;HaplotypeScore=910.2406;MQ=60.00;MQ0=0;QD=2.14;SB=-66.39;VQSLOD=-4.0875;sumGLbyD=2.30	GT:AD:DP:GQ:PL	0/1:82,41:90:99:427,0,898
-20	29421517	.	C	A	431.45	PASS	AC=1;AF=0.50;AN=2;DP=184;DS;Dels=0.07;HRun=1;HaplotypeScore=355.9651;MQ=60.00;MQ0=0;QD=2.34;SB=-209.51;VQSLOD=-1.2380;sumGLbyD=2.51	GT:AD:DP:GQ:PL	0/1:111,44:136:99:461,0,1757
-20	29421536	.	T	G	264.10	PASS	AC=1;AF=0.50;AN=2;DP=178;DS;Dels=0.00;HRun=0;HaplotypeScore=305.4345;MQ=60.00;MQ0=0;QD=1.48;SB=-87.93;VQSLOD=-1.2199;sumGLbyD=1.65	GT:AD:DP:GQ:PL	0/1:146,31:77:99:294,0,1004
-20	29421563	rs4892327	T	C	322.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=173;DS;Dels=0.01;HRun=0;HaplotypeScore=136.6393;MQ=60.00;MQ0=0;QD=1.86;SB=-164.90;VQSLOD=-0.8402;sumGLbyD=2.04	GT:AD:DP:GQ:PL	0/1:129,39:93:99:352,0,1199
-20	29421583	rs4892353	T	A	299.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=166;DS;Dels=0.02;HRun=0;HaplotypeScore=184.7619;MQ=60.00;MQ0=0;QD=1.80;SB=-103.61;VQSLOD=-0.7616;sumGLbyD=1.98	GT:AD:DP:GQ:PL	0/1:118,42:107:99:329,0,1580
-20	29421738	rs62199554	A	T	150.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=122;DS;Dels=0.11;HRun=2;HaplotypeScore=266.3549;MQ=60.00;MQ0=0;QD=1.23;SB=-81.84;VQSLOD=-2.1938;sumGLbyD=1.48	GT:AD:DP:GQ:PL	0/1:83,21:86:99:180,0,1248
-20	29421748	rs62199555	T	G	576.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=121;DS;Dels=0.01;HRun=0;HaplotypeScore=129.6836;MQ=60.00;MQ0=0;QD=4.77;SB=-201.20;VQSLOD=-0.5431;sumGLbyD=5.01	GT:AD:DP:GQ:PL	0/1:69,49:82:99:607,0,754
-20	29421776	rs62199556	C	T	92.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=118;DS;Dels=0.13;HRun=2;HaplotypeScore=236.0217;MQ=60.00;MQ0=0;QD=0.79;SB=-22.99;VQSLOD=-2.6946;sumGLbyD=1.04	GT:AD:DP:GQ:PL	0/1:86,17:62:99:123,0,926
-20	29421878	.	G	A	425.76	PASS	AC=1;AF=0.50;AN=2;DP=98;DS;Dels=0.07;HRun=0;HaplotypeScore=196.1537;MQ=60.00;MQ0=0;QD=4.34;SB=-215.43;VQSLOD=-0.4077;sumGLbyD=4.65	GT:AD:DP:GQ:PL	0/1:43,38:58:99:456,0,530
-20	29421881	.	A	T	197.01	PASS	AC=1;AF=0.50;AN=2;DP=98;DS;Dels=0.00;HRun=0;HaplotypeScore=114.6427;MQ=60.00;MQ0=0;QD=2.01;SB=-82.32;VQSLOD=-1.0732;sumGLbyD=2.32	GT:AD:DP:GQ:PL	0/1:74,22:48:99:227,0,548
-20	29421905	.	G	A	385.04	PASS	AC=1;AF=0.50;AN=2;DP=95;DS;Dels=0.04;HRun=0;HaplotypeScore=125.2942;MQ=60.00;MQ0=0;QD=4.05;SB=-196.51;VQSLOD=-0.2932;sumGLbyD=4.37	GT:AD:DP:GQ:PL	0/1:43,38:54:99:415,0,381
-20	29435222	rs4086596	T	A	114.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=22;Dels=0.05;HRun=1;HaplotypeScore=23.4028;MQ=60.00;MQ0=0;QD=5.21;SB=-47.06;VQSLOD=-3.3077;sumGLbyD=6.57	GT:AD:DP:GQ:PL	0/1:8,9:15:81.55:145,0,82
-20	29435284	.	C	T	48.83	PASS	AC=1;AF=0.50;AN=2;DP=26;Dels=0.04;HRun=0;HaplotypeScore=22.5886;MQ=60.00;MQ0=0;QD=1.88;SB=-22.48;VQSLOD=-2.5921;sumGLbyD=3.03	GT:AD:DP:GQ:PL	0/1:17,8:22:78.82:79,0,251
-20	29435287	rs4086594	C	G	43.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=26;Dels=0.12;HRun=0;HaplotypeScore=39.8014;MQ=60.00;MQ0=0;QD=1.67;SB=-20.42;VQSLOD=-2.5130;sumGLbyD=2.83	GT:AD:DP:GQ:PL	0/1:14,9:16:73.53:74,0,216
-20	29435563	rs13045694	G	A	220.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.03;HRun=0;HaplotypeScore=56.3491;MQ=60.00;MQ0=0;QD=5.50;SB=-88.47;VQSLOD=-1.6708;sumGLbyD=6.25	GT:AD:DP:GQ:PL	0/1:18,18:21:99:250,0,121
-20	29435578	rs13043873	C	A	102.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.13;HRun=1;HaplotypeScore=106.4052;MQ=60.00;MQ0=0;QD=2.56;SB=-44.16;VQSLOD=-2.2344;sumGLbyD=3.31	GT:AD:DP:GQ:PL	0/1:22,11:28:99:132,0,344
-20	29435635	.	G	A	30.40	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.15;HRun=0;HaplotypeScore=96.1335;MQ=60.00;MQ0=0;QD=0.74;SB=-20.42;VQSLOD=-2.4163;sumGLbyD=1.47	GT:AD:DP:GQ:PL	0/1:27,7:31:60.39:60,0,466
-20	29435660	rs13045968	A	G	322.13	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.19;HRun=1;HaplotypeScore=115.5873;MQ=60.00;MQ0=0;QD=7.49;SB=-72.77;VQSLOD=-1.9071;sumGLbyD=8.19	GT:AD:DP:GQ:PL	0/1:12,21:27:88.09:352,0,88
-20	29435686	rs13036813	T	C	188.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;Dels=0.07;HRun=0;HaplotypeScore=79.2513;MQ=60.00;MQ0=0;QD=4.09;SB=-81.50;VQSLOD=-1.0253;sumGLbyD=4.74	GT:AD:DP:GQ:PL	0/1:20,22:30:99:218,0,242
-20	29435702	rs13036824	T	G	70.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=48;Dels=0.00;HRun=1;HaplotypeScore=34.6042;MQ=60.00;MQ0=0;QD=1.47;SB=-16.52;VQSLOD=-3.3206;sumGLbyD=2.10	GT:AD:DP:GQ:PL	0/1:35,13:36:99:101,0,514
-20	29435746	rs13044090	C	T	316.22	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.06;HRun=0;HaplotypeScore=70.6853;MQ=60.00;MQ0=0;QD=6.32;SB=-59.82;VQSLOD=-1.9571;sumGLbyD=6.92	GT:AD:DP:GQ:PL	0/1:17,27:34:99:346,0,253
-20	29435832	rs13040301	G	A	239.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.08;HRun=1;HaplotypeScore=104.9138;MQ=60.00;MQ0=0;QD=4.07;SB=-104.52;VQSLOD=-1.7950;sumGLbyD=4.57	GT:AD:DP:GQ:PL	0/1:26,21:45:99:270,0,473
-20	29435854	rs13040308	G	T	133.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=64;Dels=0.05;HRun=0;HaplotypeScore=51.7621;MQ=60.00;MQ0=0;QD=2.09;SB=-42.73;VQSLOD=-1.9053;sumGLbyD=2.55	GT:AD:DP:GQ:PL	0/1:42,16:50:99:163,0,714
-20	29435887	rs13037177	T	C	286.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.02;HRun=0;HaplotypeScore=71.2934;MQ=60.00;MQ0=0;QD=4.34;SB=-84.18;VQSLOD=-1.1350;sumGLbyD=4.79	GT:AD:DP:GQ:PL	0/1:33,26:48:99:316,0,442
-20	29435941	rs13037204	T	C	146.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=67;Dels=0.00;HRun=0;HaplotypeScore=69.6146;MQ=60.00;MQ0=0;QD=2.19;SB=-54.89;VQSLOD=-1.5516;sumGLbyD=2.64	GT:AD:DP:GQ:PL	0/1:50,16:29:99:177,0,315
-20	29436064	.	A	T	41.31	PASS	AC=1;AF=0.50;AN=2;DP=72;Dels=0.07;HRun=2;HaplotypeScore=116.9501;MQ=60.00;MQ0=0;QD=0.57;SB=-3.98;VQSLOD=-3.6017;sumGLbyD=0.99	GT:AD:DP:GQ:PL	0/1:57,10:54:71.31:71,0,880
-20	29436082	.	C	T	35.69	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=2;HaplotypeScore=61.3692;MQ=60.00;MQ0=0;QD=0.49;SB=-23.15;VQSLOD=-4.1195;sumGLbyD=0.90	GT:AD:DP:GQ:PL	0/1:58,14:46:65.68:66,0,715
-20	29436086	.	C	A	86.37	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.00;HRun=0;HaplotypeScore=84.7886;MQ=60.00;MQ0=0;QD=1.18;SB=-49.81;VQSLOD=-2.1138;sumGLbyD=1.59	GT:AD:DP:GQ:PL	0/1:51,17:44:99:116,0,613
-20	29436112	rs3954509	C	T	142.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.07;HRun=1;HaplotypeScore=109.7596;MQ=60.00;MQ0=0;QD=1.98;SB=-11.33;VQSLOD=-2.5756;sumGLbyD=2.40	GT:AD:DP:GQ:PL	0/1:44,19:38:99:173,0,454
-20	29436239	rs4010657	T	C	159.73	PASS	AC=1;AF=0.50;AN=2;DB;DP=53;Dels=0.06;HRun=0;HaplotypeScore=92.7959;MQ=60.00;MQ0=0;QD=3.01;SB=-93.08;VQSLOD=-0.7822;sumGLbyD=3.58	GT:AD:DP:GQ:PL	0/1:32,17:31:99:190,0,335
-20	29436241	.	A	G	47.74	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.06;HRun=0;HaplotypeScore=87.8653;MQ=60.00;MQ0=0;QD=0.90;SB=-38.11;VQSLOD=-2.3332;sumGLbyD=1.47	GT:AD:DP:GQ:PL	0/1:39,11:37:77.73:78,0,580
-20	29436319	.	T	C	54.63	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=1;HaplotypeScore=36.4307;MQ=60.00;MQ0=0;QD=1.16;SB=-38.13;VQSLOD=-3.2372;sumGLbyD=1.80	GT:AD:DP:GQ:PL	0/1:32,12:33:84.62:85,0,475
-20	29436447	.	A	G	31.74	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=32.2553;MQ=60.00;MQ0=0;QD=0.81;SB=-20.44;VQSLOD=-3.2212;sumGLbyD=1.58	GT:AD:DP:GQ:PL	0/1:28,10:20:61.73:62,0,275
-20	29436449	.	T	C	74.80	PASS	AC=1;AF=0.50;AN=2;DP=39;Dels=0.00;HRun=0;HaplotypeScore=31.7694;MQ=60.00;MQ0=0;QD=1.92;SB=-22.52;VQSLOD=-2.4372;sumGLbyD=2.69	GT:AD:DP:GQ:PL	0/1:26,12:28:99:105,0,356
-20	29440028	rs6057385	G	A	136.06	PASS	AC=1;AF=0.50;AN=2;DB;DP=37;Dels=0.05;HRun=0;HaplotypeScore=47.4052;MQ=60.00;MQ0=0;QD=3.68;SB=-23.41;VQSLOD=-1.7684;sumGLbyD=4.49	GT:AD:DP:GQ:PL	0/1:24,11:26:99:166,0,297
-20	29440074	.	G	T	81.76	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.12;HRun=0;HaplotypeScore=96.9707;MQ=60.00;MQ0=0;QD=1.99;SB=-41.11;VQSLOD=-1.4973;sumGLbyD=2.73	GT:AD:DP:GQ:PL	0/1:21,13:27:99:112,0,369
-20	29440159	rs6141209	A	T	41.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.00;HRun=1;HaplotypeScore=57.6174;MQ=60.00;MQ0=0;QD=0.55;SB=-0.07;VQSLOD=-3.6406;sumGLbyD=0.94	GT:AD:DP:GQ:PL	0/1:64,12:55:71.64:72,0,898
-20	29440368	.	C	A	95.09	PASS	AC=1;AF=0.50;AN=2;DP=107;Dels=0.10;HRun=0;HaplotypeScore=182.2235;MQ=60.00;MQ0=0;QD=0.89;SB=-19.69;VQSLOD=-1.6800;sumGLbyD=1.17	GT:AD:DP:GQ:PL	0/1:75,19:78:99:125,0,1199
-20	29440484	rs6118917	C	T	237.39	PASS	AC=1;AF=0.50;AN=2;DB;DP=120;Dels=0.18;HRun=4;HaplotypeScore=310.4710;MQ=60.00;MQ0=0;QD=1.98;SB=-99.72;VQSLOD=-7.1789;sumGLbyD=2.23	GT:AD:DP:GQ:PL	0/1:73,23:70:99:267,0,923
-20	29440573	rs4086767	A	G	85.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=135;Dels=0.00;HRun=0;HaplotypeScore=138.4102;MQ=60.00;MQ0=0;QD=0.63;SB=-51.44;VQSLOD=-1.9480;sumGLbyD=0.86	GT:AD:DP:GQ:PL	0/1:109,25:102:99:116,0,1586
-20	29440666	.	G	T	129.59	PASS	AC=1;AF=0.50;AN=2;DP=142;Dels=0.07;HRun=0;HaplotypeScore=242.7720;MQ=60.00;MQ0=0;QD=0.91;SB=-57.53;VQSLOD=-1.3668;sumGLbyD=1.12	GT:AD:DP:GQ:PL	0/1:105,26:108:99:160,0,1778
-20	29440727	.	G	A	114.13	PASS	AC=1;AF=0.50;AN=2;DP=146;Dels=0.04;HRun=0;HaplotypeScore=167.4264;MQ=60.00;MQ0=0;QD=0.78;SB=-71.61;VQSLOD=-1.5915;sumGLbyD=0.99	GT:AD:DP:GQ:PL	0/1:106,23:102:99:144,0,1341
-20	29440763	rs6119110	A	G	154.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=157;Dels=0.10;HRun=1;HaplotypeScore=316.2624;MQ=60.00;MQ0=0;QD=0.98;SB=-63.70;VQSLOD=-2.2437;sumGLbyD=1.17	GT:AD:DP:GQ:PL	0/1:110,27:113:99:184,0,1858
-20	29440821	rs6118918	T	C	47.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=156;Dels=0.10;HRun=1;HaplotypeScore=304.6524;MQ=60.00;MQ0=0;QD=0.30;SB=-22.64;VQSLOD=-2.8762;sumGLbyD=0.50	GT:AD:DP:GQ:PL	0/1:117,22:104:77.49:77,0,1739
-20	29440826	.	G	A	97.64	PASS	AC=1;AF=0.50;AN=2;DP=157;Dels=0.00;HRun=3;HaplotypeScore=154.4415;MQ=60.00;MQ0=0;QD=0.62;SB=3.81;VQSLOD=-5.4274;sumGLbyD=0.81	GT:AD:DP:GQ:PL	0/1:127,28:110:99:128,0,1686
-20	29440930	.	C	T	65.37	PASS	AC=1;AF=0.50;AN=2;DP=142;Dels=0.00;HRun=0;HaplotypeScore=103.0543;MQ=60.00;MQ0=0;QD=0.46;SB=-25.04;VQSLOD=-2.4628;sumGLbyD=0.67	GT:AD:DP:GQ:PL	0/1:115,21:95:95.36:95,0,1503
-20	29441048	rs6119117	G	A	159.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=106;Dels=0.08;HRun=1;HaplotypeScore=211.3577;MQ=60.00;MQ0=0;QD=1.51;SB=-82.01;VQSLOD=-1.8052;sumGLbyD=1.79	GT:AD:DP:GQ:PL	0/1:69,27:60:99:190,0,857
-20	29441057	.	C	T	45.77	PASS	AC=1;AF=0.50;AN=2;DP=102;Dels=0.11;HRun=2;HaplotypeScore=254.0858;MQ=60.00;MQ0=0;QD=0.45;SB=-17.68;VQSLOD=-2.8922;sumGLbyD=0.74	GT:AD:DP:GQ:PL	0/1:75,14:59:75.76:76,0,976
-20	29441058	.	A	G	35.57	PASS	AC=1;AF=0.50;AN=2;DP=102;Dels=0.05;HRun=2;HaplotypeScore=184.3128;MQ=60.00;MQ0=0;QD=0.35;SB=-13.57;VQSLOD=-3.1954;sumGLbyD=0.64	GT:AD:DP:GQ:PL	0/1:73,16:61:65.56:66,0,1035
-20	29441113	.	T	C	105.81	PASS	AC=1;AF=0.50;AN=2;DP=83;Dels=0.00;HRun=0;HaplotypeScore=88.3146;MQ=60.00;MQ0=0;QD=1.27;SB=-30.04;VQSLOD=-2.1209;sumGLbyD=1.64	GT:AD:DP:GQ:PL	0/1:66,15:51:99:136,0,747
-20	29447572	rs4010649	T	A	61.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=58;Dels=0.03;HRun=0;HaplotypeScore=86.1321;MQ=60.00;MQ0=0;QD=1.06;SB=-25.93;VQSLOD=-2.3107;sumGLbyD=1.58	GT:AD:DP:GQ:PL	0/1:44,11:44:91.49:91,0,694
-20	29447740	rs4010646	G	A	62.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.10;HRun=1;HaplotypeScore=136.5688;MQ=60.00;MQ0=0;QD=0.86;SB=-18.84;VQSLOD=-2.7017;sumGLbyD=1.28	GT:AD:DP:GQ:PL	0/1:47,14:53:92.21:92,0,773
-20	29447862	rs6141222	T	C	234.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.03;HRun=0;HaplotypeScore=110.1220;MQ=60.00;MQ0=0;QD=2.61;SB=-62.50;VQSLOD=-0.9723;sumGLbyD=2.94	GT:AD:DP:GQ:PL	0/1:63,23:68:99:265,0,949
-20	29447981	rs6567468	G	A	57.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.15;HRun=4;HaplotypeScore=240.8423;MQ=60.00;MQ0=0;QD=0.57;SB=-28.49;VQSLOD=-8.3275;sumGLbyD=0.86	GT:AD:DP:GQ:PL	0/1:74,12:66:87.09:87,0,1046
-20	29448031	.	T	A	48.46	PASS	AC=1;AF=0.50;AN=2;DP=110;Dels=0.02;HRun=0;HaplotypeScore=105.5435;MQ=60.00;MQ0=0;QD=0.44;SB=-21.35;VQSLOD=-2.4574;sumGLbyD=0.71	GT:AD:DP:GQ:PL	0/1:90,17:88:78.46:78,0,1459
-20	29448036	.	G	C	38.40	PASS	AC=1;AF=0.50;AN=2;DP=111;Dels=0.05;HRun=0;HaplotypeScore=165.9211;MQ=60.00;MQ0=0;QD=0.35;SB=-18.06;VQSLOD=-1.9842;sumGLbyD=0.62	GT:AD:DP:GQ:PL	0/1:85,17:88:68.39:68,0,1482
-20	29448217	rs6423661	T	G	81.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=124;Dels=0.06;HRun=0;HaplotypeScore=139.7432;MQ=60.00;MQ0=0;QD=0.65;SB=18.06;VQSLOD=-2.2475;sumGLbyD=0.90	GT:AD:DP:GQ:PL	0/1:94,23:79:99:111,0,1254
-20	29448473	rs28734128	A	G	71.95	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.03;HRun=0;HaplotypeScore=66.7382;MQ=60.00;MQ0=0;QD=0.99;SB=-47.51;VQSLOD=-2.4903;sumGLbyD=1.40	GT:AD:DP:GQ:PL	0/1:52,17:46:99:102,0,688
-20	29448653	rs55794013	A	C	66.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=50;Dels=0.08;HRun=0;HaplotypeScore=90.3201;MQ=60.00;MQ0=0;QD=1.34;SB=-32.02;VQSLOD=-2.0385;sumGLbyD=1.94	GT:AD:DP:GQ:PL	0/1:36,9:33:96.83:97,0,459
-20	29452967	rs6057198	T	C	145.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.21;HRun=0;HaplotypeScore=181.0850;MQ=60.00;MQ0=0;QD=2.80;SB=-44.09;VQSLOD=-0.9365;sumGLbyD=3.38	GT:AD:DP:GQ:PL	0/1:18,18:28:99:176,0,244
-20	29453501	rs6119151	C	A	702.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=146;Dels=0.10;HRun=0;HaplotypeScore=263.5570;MQ=60.00;MQ0=0;QD=4.81;SB=-297.40;VQSLOD=-0.8374;sumGLbyD=5.01	GT:AD:DP:GQ:PL	0/1:80,49:111:99:732,0,1254
-20	29453559	rs6119152	T	C	341.41	PASS	AC=1;AF=0.50;AN=2;DB;DP=140;Dels=0.04;HRun=0;HaplotypeScore=176.2529;MQ=60.00;MQ0=0;QD=2.44;SB=-173.82;VQSLOD=-0.3295;sumGLbyD=2.65	GT:AD:DP:GQ:PL	0/1:84,45:87:99:371,0,1124
-20	29467416	.	G	A	142.07	PASS	AC=1;AF=0.50;AN=2;DP=40;Dels=0.00;HRun=0;HaplotypeScore=25.5433;MQ=60.00;MQ0=0;QD=3.55;SB=-71.02;VQSLOD=-1.5184;sumGLbyD=4.30	GT:AD:DP:GQ:PL	0/1:25,15:32:99:172,0,363
-20	29467503	rs34728591	T	C	107.10	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.05;HRun=0;HaplotypeScore=57.3750;MQ=60.00;MQ0=0;QD=2.68;SB=-67.68;VQSLOD=-1.3644;sumGLbyD=3.43	GT:AD:DP:GQ:PL	0/1:19,15:24:99:137,0,229
-20	29467558	rs34262406	A	G	70.47	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.05;HRun=0;HaplotypeScore=69.9752;MQ=60.00;MQ0=0;QD=1.76;SB=-2.64;VQSLOD=-2.2359;sumGLbyD=2.51	GT:AD:DP:GQ:PL	0/1:20,17:24:99:100,0,316
-20	29467576	rs35459740	A	T	181.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;Dels=0.07;HRun=2;HaplotypeScore=65.3878;MQ=60.00;MQ0=0;QD=4.44;SB=-36.40;VQSLOD=-3.6145;sumGLbyD=5.17	GT:AD:DP:GQ:PL	0/1:16,22:26:99:212,0,241
-20	29467584	.	T	C	139.06	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.00;HRun=0;HaplotypeScore=43.9104;MQ=60.00;MQ0=0;QD=3.39;SB=-32.45;VQSLOD=-1.6785;sumGLbyD=4.12	GT:AD:DP:GQ:PL	0/1:31,10:23:99:169,0,216
-20	29467604	rs11152475	A	C	143.97	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.26;HRun=2;HaplotypeScore=179.9714;MQ=60.00;MQ0=0;QD=3.43;SB=-27.42;VQSLOD=-2.4633;sumGLbyD=4.14	GT:AD:DP:GQ:PL	0/1:16,12:24:99:174,0,248
-20	29467639	rs34304717	G	A	132.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=1;HaplotypeScore=35.8612;MQ=60.00;MQ0=0;QD=3.08;SB=-56.76;VQSLOD=-2.7353;sumGLbyD=3.78	GT:AD:DP:GQ:PL	0/1:29,12:38:99:163,0,488
-20	29467733	rs11699875	G	T	80.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.15;HRun=1;HaplotypeScore=137.3785;MQ=60.00;MQ0=0;QD=1.55;SB=-48.67;VQSLOD=-2.1971;sumGLbyD=2.12	GT:AD:DP:GQ:PL	0/1:33,11:32:99:110,0,429
-20	29467782	rs11698482	A	C	164.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.00;HRun=0;HaplotypeScore=63.1712;MQ=60.00;MQ0=0;QD=2.39;SB=-56.73;VQSLOD=-1.5047;sumGLbyD=2.82	GT:AD:DP:GQ:PL	0/1:46,22:52:99:195,0,714
-20	29467811	rs11698485	A	G	168.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.08;HRun=1;HaplotypeScore=140.5340;MQ=60.00;MQ0=0;QD=2.19;SB=-98.83;VQSLOD=-1.7027;sumGLbyD=2.58	GT:AD:DP:GQ:PL	0/1:43,17:49:99:199,0,491
-20	29467841	rs10871839	A	C	270.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=80;Dels=0.04;HRun=0;HaplotypeScore=83.3068;MQ=60.00;MQ0=0;QD=3.38;SB=-144.40;VQSLOD=-0.5710;sumGLbyD=3.75	GT:AD:DP:GQ:PL	0/1:40,29:51:99:300,0,590
-20	29468001	rs11698520	A	G	631.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=212;Dels=0.02;HRun=0;HaplotypeScore=171.5039;MQ=60.00;MQ0=0;QD=2.98;SB=-172.24;VQSLOD=-0.1855;sumGLbyD=3.12	GT:AD:DP:GQ:PL	0/1:120,76:154:99:661,0,1898
-20	29468105	rs10871840	G	T	654.29	PASS	AC=1;AF=0.50;AN=2;DB;DP=231;Dels=0.00;HRun=1;HaplotypeScore=183.8367;MQ=60.00;MQ0=0;QD=2.83;SB=-293.05;VQSLOD=-1.4589;sumGLbyD=2.96	GT:AD:DP:GQ:PL	0/1:155,74:162:99:684,0,1969
-20	29468126	rs6057457	A	T	921.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=234;Dels=0.21;HRun=3;HaplotypeScore=710.9124;MQ=60.00;MQ0=0;QD=3.94;SB=-383.51;VQSLOD=-2.5668;sumGLbyD=4.07	GT:AD:DP:GQ:PL	0/1:102,77:147:99:952,0,1535
-20	29468186	rs10871841	T	C	461.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=249;DS;Dels=0.00;HRun=0;HaplotypeScore=155.1526;MQ=60.00;MQ0=0;QD=1.86;SB=-182.46;VQSLOD=-0.7522;sumGLbyD=1.98	GT:AD:DP:GQ:PL	0/1:187,54:167:99:492,0,2366
-20	29468203	rs34667336	A	G	502.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=245;DS;Dels=0.02;HRun=0;HaplotypeScore=228.7433;MQ=60.00;MQ0=0;QD=2.05;SB=-213.22;VQSLOD=-0.5376;sumGLbyD=2.17	GT:AD:DP:GQ:PL	0/1:155,73:170:99:532,0,2314
-20	29468231	rs10871842	C	T	875.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=244;DS;Dels=0.01;HRun=0;HaplotypeScore=235.0552;MQ=60.00;MQ0=0;QD=3.59;SB=-427.54;VQSLOD=-0.6177;sumGLbyD=3.71	GT:AD:DP:GQ:PL	0/1:160,75:176:99:906,0,1766
-20	29468320	.	A	G	469.33	PASS	AC=1;AF=0.50;AN=2;DP=245;DS;Dels=0.00;HRun=1;HaplotypeScore=224.8774;MQ=60.00;MQ0=0;QD=1.92;SB=-165.19;VQSLOD=-1.4216;sumGLbyD=2.04	GT:AD:DP:GQ:PL	0/1:186,56:170:99:499,0,2440
-20	29468365	rs11152476	T	G	609.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=240;DS;Dels=0.08;HRun=1;HaplotypeScore=491.7721;MQ=60.00;MQ0=0;QD=2.54;SB=-110.80;VQSLOD=-1.1979;sumGLbyD=2.67	GT:AD:DP:GQ:PL	0/1:147,69:173:99:640,0,2399
-20	29468368	rs6118940	G	A	115.68	PASS	AC=1;AF=0.50;AN=2;DB;DP=239;DS;Dels=0.06;HRun=1;HaplotypeScore=432.2931;MQ=60.00;MQ0=0;QD=0.48;SB=20.34;VQSLOD=-3.3846;sumGLbyD=0.61	GT:AD:DP:GQ:PL	0/1:184,32:182:99:146,0,2907
-20	29468391	rs6057458	T	C	1044.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=246;DS;Dels=0.00;HRun=1;HaplotypeScore=240.2562;MQ=60.00;MQ0=0;QD=4.25;SB=-368.30;VQSLOD=-1.8126;sumGLbyD=4.37	GT:AD:DP:GQ:PL	0/1:147,91:157:99:1074,0,1559
-20	29468489	rs11152479	T	G	526.63	PASS	AC=1;AF=0.50;AN=2;DB;DP=244;DS;Dels=0.06;HRun=0;HaplotypeScore=416.0168;MQ=60.00;MQ0=0;QD=2.16;SB=-132.38;VQSLOD=-1.1063;sumGLbyD=2.28	GT:AD:DP:GQ:PL	0/1:143,74:147:99:557,0,1955
-20	29468534	rs6087321	T	C	295.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=246;DS;Dels=0.15;HRun=1;HaplotypeScore=625.2170;MQ=60.00;MQ0=0;QD=1.20;SB=-124.62;VQSLOD=-1.6664;sumGLbyD=1.32	GT:AD:DP:GQ:PL	0/1:161,46:145:99:325,0,2142
-20	29468554	rs11152480	A	G	993.12	PASS	AC=1;AF=0.50;AN=2;DB;DP=242;DS;Dels=0.02;HRun=0;HaplotypeScore=183.1852;MQ=60.00;MQ0=0;QD=4.10;SB=-396.40;VQSLOD=-0.6666;sumGLbyD=4.23	GT:AD:DP:GQ:PL	0/1:144,91:182:99:1023,0,2166
-20	29468603	rs11152481	A	G	805.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=245;DS;Dels=0.06;HRun=1;HaplotypeScore=312.6950;MQ=60.00;MQ0=0;QD=3.29;SB=-318.49;VQSLOD=-1.7374;sumGLbyD=3.41	GT:AD:DP:GQ:PL	0/1:150,75:168:99:835,0,2176
-20	29468690	rs8184144	A	C	643.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=231;DS;Dels=0.06;HRun=0;HaplotypeScore=329.3029;MQ=60.00;MQ0=0;QD=2.79;SB=-285.94;VQSLOD=-0.7504;sumGLbyD=2.92	GT:AD:DP:GQ:PL	0/1:119,80:151:99:674,0,1691
-20	29468796	rs10747227	C	G	832.24	PASS	AC=1;AF=0.50;AN=2;DB;DP=212;DS;Dels=0.01;HRun=0;HaplotypeScore=210.3980;MQ=60.00;MQ0=0;QD=3.93;SB=-399.69;VQSLOD=-0.5483;sumGLbyD=4.07	GT:AD:DP:GQ:PL	0/1:116,81:133:99:862,0,1467
-20	29468956	rs10747228	G	A	82.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=104;DS;Dels=0.14;HRun=4;HaplotypeScore=253.3276;MQ=60.00;MQ0=0;QD=0.79;SB=-31.07;VQSLOD=-8.0987;sumGLbyD=1.08	GT:AD:DP:GQ:PL	0/1:46,36:42:99:112,0,585
-20	29469091	rs10871843	G	A	283.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;DS;Dels=0.13;HRun=1;HaplotypeScore=190.9904;MQ=60.00;MQ0=0;QD=3.99;SB=-153.89;VQSLOD=-1.1620;sumGLbyD=4.41	GT:AD:DP:GQ:PL	0/1:37,24:39:99:313,0,363
-20	29469094	rs10871844	A	G	63.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;DS;Dels=0.25;HRun=1;HaplotypeScore=307.5404;MQ=60.00;MQ0=0;QD=0.89;SB=-44.55;VQSLOD=-2.4033;sumGLbyD=1.31	GT:AD:DP:GQ:PL	0/1:38,14:35:93.31:93,0,498
-20	29469108	rs10782072	G	T	176.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;DS;Dels=0.26;HRun=2;HaplotypeScore=288.5705;MQ=60.00;MQ0=0;QD=2.56;SB=-35.90;VQSLOD=-2.1413;sumGLbyD=2.99	GT:AD:DP:GQ:PL	0/1:31,17:45:99:206,0,549
-20	29469189	rs10871845	A	C	148.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=61;DS;Dels=0.20;HRun=1;HaplotypeScore=203.3645;MQ=60.00;MQ0=0;QD=2.44;SB=-43.20;VQSLOD=-1.8779;sumGLbyD=2.93	GT:AD:DP:GQ:PL	0/1:31,15:34:99:179,0,384
-20	29469273	.	C	T	139.01	PASS	AC=1;AF=0.50;AN=2;DP=51;DS;Dels=0.12;HRun=4;HaplotypeScore=98.5108;MQ=60.00;MQ0=0;QD=2.73;SB=5.28;VQSLOD=-9.2241;sumGLbyD=3.31	GT:AD:DP:GQ:PL	0/1:26,19:24:99:169,0,260
-20	29469296	rs10871846	A	G	175.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=47;DS;Dels=0.00;HRun=0;HaplotypeScore=33.8084;MQ=60.00;MQ0=0;QD=3.74;SB=-71.52;VQSLOD=-1.4204;sumGLbyD=4.37	GT:AD:DP:GQ:PL	0/1:25,21:27:99:206,0,258
-20	29469315	.	T	A	129.35	PASS	AC=1;AF=0.50;AN=2;DP=46;DS;Dels=0.00;HRun=0;HaplotypeScore=38.0687;MQ=60.00;MQ0=0;QD=2.81;SB=-47.18;VQSLOD=-1.7008;sumGLbyD=3.46	GT:AD:DP:GQ:PL	0/1:26,20:19:99:159,0,170
-20	29469319	rs12329505	T	C	204.62	PASS	AC=1;AF=0.50;AN=2;DB;DP=46;DS;Dels=0.04;HRun=0;HaplotypeScore=72.5752;MQ=60.00;MQ0=0;QD=4.45;SB=-109.27;VQSLOD=-0.9681;sumGLbyD=5.10	GT:AD:DP:GQ:PL	0/1:22,21:29:99:235,0,254
-20	29469326	.	T	C	76.92	PASS	AC=1;AF=0.50;AN=2;DP=46;DS;Dels=0.07;HRun=1;HaplotypeScore=74.1946;MQ=60.00;MQ0=0;QD=1.67;SB=-25.88;VQSLOD=-2.7787;sumGLbyD=2.32	GT:AD:DP:GQ:PL	0/1:29,13:26:99:107,0,311
-20	29469368	rs12329412	G	T	58.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=41;DS;Dels=0.12;HRun=1;HaplotypeScore=107.1426;MQ=60.00;MQ0=0;QD=1.42;SB=-29.44;VQSLOD=-2.5666;sumGLbyD=2.15	GT:AD:DP:GQ:PL	0/1:20,12:20:88.26:88,0,229
-20	29484025	rs11152494	T	G	133.20	PASS	AC=1;AF=0.50;AN=2;DB;DP=42;Dels=0.07;HRun=0;HaplotypeScore=73.5074;MQ=60.00;MQ0=0;QD=3.17;SB=-73.28;VQSLOD=-1.0432;sumGLbyD=3.89	GT:AD:DP:GQ:PL	0/1:21,18:29:99:163,0,300
-20	29484050	rs11152495	A	C	208.84	PASS	AC=1;AF=0.50;AN=2;DB;DP=49;Dels=0.00;HRun=0;HaplotypeScore=35.6165;MQ=60.00;MQ0=0;QD=4.26;SB=-21.21;VQSLOD=-2.0624;sumGLbyD=4.87	GT:AD:DP:GQ:PL	0/1:29,20:31:99:239,0,282
-20	29484080	.	A	G	98.89	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.04;HRun=0;HaplotypeScore=72.7739;MQ=60.00;MQ0=0;QD=1.87;SB=-44.63;VQSLOD=-1.7830;sumGLbyD=2.43	GT:AD:DP:GQ:PL	0/1:34,16:44:99:129,0,659
-20	29484150	rs57119699	G	A	412.94	PASS	AC=1;AF=0.50;AN=2;DB;DP=69;Dels=0.12;HRun=0;HaplotypeScore=198.4329;MQ=60.00;MQ0=0;QD=5.98;SB=-172.24;VQSLOD=-1.2557;sumGLbyD=6.42	GT:AD:DP:GQ:PL	0/1:19,42:37:99:443,0,144
-20	29484157	rs59400032	A	G	75.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.01;HRun=0;HaplotypeScore=125.5629;MQ=60.00;MQ0=0;QD=1.05;SB=-29.21;VQSLOD=-1.9033;sumGLbyD=1.47	GT:AD:DP:GQ:PL	0/1:51,20:36:99:106,0,488
-20	29484167	rs60417788	A	G	181.81	PASS	AC=1;AF=0.50;AN=2;DB;DP=73;Dels=0.12;HRun=0;HaplotypeScore=179.5527;MQ=60.00;MQ0=0;QD=2.49;SB=-98.88;VQSLOD=-0.5265;sumGLbyD=2.90	GT:AD:DP:GQ:PL	0/1:34,25:41:99:212,0,509
-20	29484192	rs11152496	T	C	505.61	PASS	AC=1;AF=0.50;AN=2;DB;DP=76;Dels=0.01;HRun=0;HaplotypeScore=88.5834;MQ=60.00;MQ0=0;QD=6.65;SB=-259.35;VQSLOD=-1.4894;sumGLbyD=7.05	GT:AD:DP:GQ:PL	0/1:33,39:51:99:536,0,315
-20	29484318	rs10871847	A	G	380.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=98;Dels=0.06;HRun=0;HaplotypeScore=164.7363;MQ=60.00;MQ0=0;QD=3.89;SB=-138.70;VQSLOD=-0.3773;sumGLbyD=4.19	GT:AD:DP:GQ:PL	0/1:52,35:74:99:411,0,911
-20	29484358	rs10871848	C	G	514.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=105;Dels=0.02;HRun=0;HaplotypeScore=82.6285;MQ=60.00;MQ0=0;QD=4.90;SB=-244.37;VQSLOD=-0.7824;sumGLbyD=5.18	GT:AD:DP:GQ:PL	0/1:63,39:84:99:544,0,957
-20	29484378	.	C	T	41.07	PASS	AC=1;AF=0.50;AN=2;DP=107;Dels=0.13;HRun=0;HaplotypeScore=255.4483;MQ=60.00;MQ0=0;QD=0.38;SB=-33.54;VQSLOD=-1.6334;sumGLbyD=0.66	GT:AD:DP:GQ:PL	0/1:78,14:73:71.06:71,0,1144
-20	29484449	rs10871849	T	C	335.46	PASS	AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.00;HRun=1;HaplotypeScore=200.7170;MQ=60.00;MQ0=0;QD=2.50;SB=-144.81;VQSLOD=-1.3014;sumGLbyD=2.73	GT:AD:DP:GQ:PL	0/1:96,36:81:99:365,0,1031
-20	29484555	rs10871850	T	C	400.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.09;HRun=0;HaplotypeScore=305.4738;MQ=60.00;MQ0=0;QD=2.37;SB=-65.04;VQSLOD=-1.3396;sumGLbyD=2.55	GT:AD:DP:GQ:PL	0/1:97,52:119:99:430,0,1549
-20	29484559	rs10871851	T	A	623.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=169;Dels=0.04;HRun=1;HaplotypeScore=222.0270;MQ=60.00;MQ0=0;QD=3.69;SB=-193.92;VQSLOD=-1.1331;sumGLbyD=3.87	GT:AD:DP:GQ:PL	0/1:104,58:131:99:654,0,1551
-20	29484681	rs10871852	G	C	914	PASS	AC=1;AF=0.50;AN=2;DB;DP=193;Dels=0.04;HRun=0;HaplotypeScore=262.0113;MQ=60.00;MQ0=0;QD=4.74;SB=-443.29;VQSLOD=-0.7228;sumGLbyD=4.89	GT:AD:DP:GQ:PL	0/1:105,73:145:99:944,0,1657
-20	29484775	rs11699484	G	A	426.40	PASS	AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.22;HRun=2;HaplotypeScore=638.5700;MQ=60.00;MQ0=0;QD=2.29;SB=-132.42;VQSLOD=-2.3651;sumGLbyD=2.45	GT:AD:DP:GQ:PL	0/1:98,45:109:99:456,0,1384
-20	29484785	rs10871853	C	G	490.72	PASS	AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.02;HRun=0;HaplotypeScore=266.4522;MQ=60.00;MQ0=0;QD=2.64;SB=-159.56;VQSLOD=-0.5013;sumGLbyD=2.80	GT:AD:DP:GQ:PL	0/1:99,69:107:99:521,0,1330
-20	29484788	rs10871854	G	A	705.89	PASS	AC=1;AF=0.50;AN=2;DB;DP=186;Dels=0.14;HRun=2;HaplotypeScore=493.3197;MQ=60.00;MQ0=0;QD=3.80;SB=-268.19;VQSLOD=-1.9973;sumGLbyD=3.96	GT:AD:DP:GQ:PL	0/1:84,64:118:99:736,0,1221
-20	29484842	rs11697042	T	C	329.04	PASS	AC=1;AF=0.50;AN=2;DB;DP=174;Dels=0.07;HRun=1;HaplotypeScore=304.9307;MQ=60.00;MQ0=0;QD=1.89;SB=-149.17;VQSLOD=-1.4503;sumGLbyD=2.06	GT:AD:DP:GQ:PL	0/1:116,43:105:99:359,0,1413
-20	29484862	rs11699917	C	T	827.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=171;Dels=0.05;HRun=0;HaplotypeScore=225.8625;MQ=60.00;MQ0=0;QD=4.84;SB=-362.70;VQSLOD=-0.7504;sumGLbyD=5.01	GT:AD:DP:GQ:PL	0/1:92,68:126:99:857,0,1358
-20	29484952	rs11699511	G	A	653.65	PASS	AC=1;AF=0.50;AN=2;DB;DP=147;Dels=0.06;HRun=0;HaplotypeScore=268.2608;MQ=60.00;MQ0=0;QD=4.45;SB=-251.47;VQSLOD=-0.7708;sumGLbyD=4.65	GT:AD:DP:GQ:PL	0/1:69,65:75:99:684,0,645
-20	29485105	.	C	T	147.13	PASS	AC=1;AF=0.50;AN=2;DP=88;Dels=0.09;HRun=1;HaplotypeScore=193.3848;MQ=60.00;MQ0=0;QD=1.67;SB=-32.79;VQSLOD=-2.0927;sumGLbyD=2.01	GT:AD:DP:GQ:PL	0/1:58,19:50:99:177,0,674
-20	29485118	rs6119182	T	C	550.69	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.20;HRun=1;HaplotypeScore=296.8366;MQ=60.00;MQ0=0;QD=6.48;SB=-207.92;VQSLOD=-1.8395;sumGLbyD=6.83	GT:AD:DP:GQ:PL	0/1:17,48:41:99:581,0,131
-20	29485133	.	A	G	220.46	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.06;HRun=0;HaplotypeScore=125.6259;MQ=60.00;MQ0=0;QD=2.72;SB=-103.16;VQSLOD=-0.5921;sumGLbyD=3.09	GT:AD:DP:GQ:PL	0/1:32,24:42:99:250,0,352
-20	29485166	.	G	T	70.52	PASS	AC=1;AF=0.50;AN=2;DP=74;Dels=0.11;HRun=0;HaplotypeScore=191.5841;MQ=60.00;MQ0=0;QD=0.95;SB=-8.60;VQSLOD=-1.6904;sumGLbyD=1.36	GT:AD:DP:GQ:PL	0/1:46,15:42:99:101,0,615
-20	29485172	.	A	C	83.43	PASS	AC=1;AF=0.50;AN=2;DP=73;Dels=0.32;HRun=1;HaplotypeScore=379.6985;MQ=60.00;MQ0=0;QD=1.14;SB=-50.61;VQSLOD=-2.1417;sumGLbyD=1.55	GT:AD:DP:GQ:PL	0/1:34,15:34:99:113,0,466
-20	29485174	rs6057493	A	G	214.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=1;HaplotypeScore=113.3719;MQ=60.00;MQ0=0;QD=2.99;SB=-63.76;VQSLOD=-2.0186;sumGLbyD=3.40	GT:AD:DP:GQ:PL	0/1:35,31:33:99:245,0,290
-20	29485177	.	A	G	116.66	PASS	AC=1;AF=0.50;AN=2;DP=72;Dels=0.06;HRun=0;HaplotypeScore=140.9697;MQ=60.00;MQ0=0;QD=1.62;SB=-20.16;VQSLOD=-1.5467;sumGLbyD=2.04	GT:AD:DP:GQ:PL	0/1:44,23:48:99:147,0,709
-20	29485212	.	A	G	118.51	PASS	AC=1;AF=0.50;AN=2;DP=65;Dels=0.09;HRun=0;HaplotypeScore=143.7147;MQ=60.00;MQ0=0;QD=1.82;SB=-17.15;VQSLOD=-1.4709;sumGLbyD=2.28	GT:AD:DP:GQ:PL	0/1:42,15:46:99:149,0,676
-20	29485297	.	G	C	49.22	PASS	AC=1;AF=0.50;AN=2;DP=53;Dels=0.00;HRun=0;HaplotypeScore=63.6775;MQ=60.00;MQ0=0;QD=0.93;SB=-25.46;VQSLOD=-2.6760;sumGLbyD=1.49	GT:AD:DP:GQ:PL	0/1:40,12:29:79.22:79,0,380
-20	29485305	.	T	G	106.95	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.04;HRun=0;HaplotypeScore=71.6839;MQ=60.00;MQ0=0;QD=2.10;SB=-51.27;VQSLOD=-1.6060;sumGLbyD=2.69	GT:AD:DP:GQ:PL	0/1:32,16:36:99:137,0,459
-20	29485314	.	C	T	93.47	PASS	AC=1;AF=0.50;AN=2;DP=51;Dels=0.06;HRun=3;HaplotypeScore=69.0207;MQ=60.00;MQ0=0;QD=1.83;SB=-20.42;VQSLOD=-5.6973;sumGLbyD=2.42	GT:AD:DP:GQ:PL	0/1:35,12:30:99:123,0,406
-20	29485369	.	C	A	70.83	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=68.2702;MQ=60.00;MQ0=0;QD=1.51;SB=-35.04;VQSLOD=-2.1508;sumGLbyD=2.15	GT:AD:DP:GQ:PL	0/1:35,12:31:99:101,0,436
-20	29485376	.	T	C	55.02	PASS	AC=1;AF=0.50;AN=2;DP=46;Dels=0.07;HRun=0;HaplotypeScore=86.5385;MQ=60.00;MQ0=0;QD=1.20;SB=8.52;VQSLOD=-2.4660;sumGLbyD=1.85	GT:AD:DP:GQ:PL	0/1:27,16:28:85.02:85,0,415
-20	29485461	.	C	A	94.63	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.02;HRun=0;HaplotypeScore=58.8880;MQ=60.00;MQ0=0;QD=2.31;SB=-57.84;VQSLOD=-1.5850;sumGLbyD=3.04	GT:AD:DP:GQ:PL	0/1:22,17:20:99:125,0,195
-20	29485469	.	T	A	42.23	PASS	AC=1;AF=0.50;AN=2;DP=41;Dels=0.05;HRun=1;HaplotypeScore=71.9768;MQ=60.00;MQ0=0;QD=1.03;SB=-10.41;VQSLOD=-3.1645;sumGLbyD=1.76	GT:AD:DP:GQ:PL	0/1:30,9:22:72.22:72,0,322
-20	29486860	.	T	C	106.09	PASS	AC=1;AF=0.50;AN=2;DP=36;Dels=0.00;HRun=0;HaplotypeScore=22.2115;MQ=60.00;MQ0=0;QD=2.95;SB=-44.89;VQSLOD=-1.8798;sumGLbyD=3.78	GT:AD:DP:GQ:PL	0/1:23,12:33:99:136,0,444
-20	29486903	.	G	C	137.83	PASS	AC=1;AF=0.50;AN=2;DP=42;Dels=0.00;HRun=0;HaplotypeScore=29.5092;MQ=60.00;MQ0=0;QD=3.28;SB=-51.85;VQSLOD=-1.6562;sumGLbyD=4.00	GT:AD:DP:GQ:PL	0/1:28,14:32:99:168,0,390
-20	29486905	.	G	A	92.58	PASS	AC=1;AF=0.50;AN=2;DP=42;Dels=0.05;HRun=0;HaplotypeScore=61.1930;MQ=60.00;MQ0=0;QD=2.20;SB=-52.95;VQSLOD=-1.6534;sumGLbyD=2.92	GT:AD:DP:GQ:PL	0/1:27,10:32:99:123,0,430
-20	29486940	.	T	C	108.22	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.00;HRun=0;HaplotypeScore=38.5602;MQ=60.00;MQ0=0;QD=2.30;SB=-55.84;VQSLOD=-1.8533;sumGLbyD=2.94	GT:AD:DP:GQ:PL	0/1:36,10:35:99:138,0,477
-20	29486942	.	G	C	93.18	PASS	AC=1;AF=0.50;AN=2;DP=47;Dels=0.02;HRun=0;HaplotypeScore=50.7710;MQ=60.00;MQ0=0;QD=1.98;SB=-54.69;VQSLOD=-1.9025;sumGLbyD=2.62	GT:AD:DP:GQ:PL	0/1:32,12:38:99:123,0,539
-20	29487060	.	T	C	57.98	PASS	AC=1;AF=0.50;AN=2;DP=81;Dels=0.15;HRun=1;HaplotypeScore=211.9349;MQ=60.00;MQ0=0;QD=0.72;SB=-13.02;VQSLOD=-2.5723;sumGLbyD=1.09	GT:AD:DP:GQ:PL	0/1:56,11:55:87.97:88,0,875
-20	29487080	.	T	A	152.62	PASS	AC=1;AF=0.50;AN=2;DP=85;Dels=0.00;HRun=0;HaplotypeScore=43.3131;MQ=60.00;MQ0=0;QD=1.80;SB=23.39;VQSLOD=-2.8111;sumGLbyD=2.15	GT:AD:DP:GQ:PL	0/1:60,24:67:99:183,0,986
-20	29487120	.	T	C	108.40	PASS	AC=1;AF=0.50;AN=2;DP=87;Dels=0.00;HRun=0;HaplotypeScore=59.0088;MQ=60.00;MQ0=0;QD=1.25;SB=-47.55;VQSLOD=-2.3905;sumGLbyD=1.59	GT:AD:DP:GQ:PL	0/1:73,14:55:99:138,0,785
-20	29487136	.	G	C	124.27	PASS	AC=1;AF=0.50;AN=2;DP=88;Dels=0.00;HRun=0;HaplotypeScore=68.6300;MQ=60.00;MQ0=0;QD=1.41;SB=-10.32;VQSLOD=-2.3979;sumGLbyD=1.75	GT:AD:DP:GQ:PL	0/1:64,20:66:99:154,0,900
-20	29487174	rs62198132	T	C	79.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=90;Dels=0.13;HRun=2;HaplotypeScore=233.5304;MQ=60.00;MQ0=0;QD=0.88;SB=20.43;VQSLOD=-2.9631;sumGLbyD=1.21	GT:AD:DP:GQ:PL	0/1:63,15:62:99:109,0,1002
-20	29487184	.	C	T	111.03	PASS	AC=1;AF=0.50;AN=2;DP=91;Dels=0.02;HRun=1;HaplotypeScore=108.0390;MQ=60.00;MQ0=0;QD=1.22;SB=-43.26;VQSLOD=-2.5312;sumGLbyD=1.55	GT:AD:DP:GQ:PL	0/1:63,25:66:99:141,0,976
-20	29487400	.	G	A	42.23	PASS	AC=1;AF=0.50;AN=2;DP=137;Dels=0.04;HRun=1;HaplotypeScore=180.4405;MQ=60.00;MQ0=0;QD=0.31;SB=-19.61;VQSLOD=-2.8214;sumGLbyD=0.53	GT:AD:DP:GQ:PL	0/1:109,21:110:72.22:72,0,1848
-20	29487847	.	C	A	47.31	PASS	AC=1;AF=0.50;AN=2;DP=91;Dels=0.04;HRun=0;HaplotypeScore=156.4597;MQ=60.00;MQ0=0;QD=0.52;SB=-37.63;VQSLOD=-1.9118;sumGLbyD=0.85	GT:AD:DP:GQ:PL	0/1:71,15:62:77.31:77,0,859
-20	29488046	rs7273439	A	G	142.36	PASS	AC=1;AF=0.50;AN=2;DB;DP=57;Dels=0.05;HRun=1;HaplotypeScore=70.9807;MQ=60.00;MQ0=0;QD=2.50;SB=-63.76;VQSLOD=-2.3401;sumGLbyD=3.02	GT:AD:DP:GQ:PL	0/1:28,21:29:99:172,0,260
-20	31262920	rs12480157	A	G	111.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.00;HRun=1;HaplotypeScore=82.2122;MQ=60.00;MQ0=0;QD=1.33;SB=-5.44;VQSLOD=-3.0017;sumGLbyD=1.68	GT:AD:DP:GQ:PL	0/1:63,19:61:99:141,0,918
-20	31263324	rs6141333	C	A	432.45	PASS	AC=1;AF=0.50;AN=2;DB;DP=250;DS;Dels=0.13;HRun=1;HaplotypeScore=659.1615;MQ=60.00;MQ0=0;QD=1.73;SB=-206.57;VQSLOD=-1.7971;sumGLbyD=1.85	GT:AD:DP:GQ:PL	0/1:155,58:137:99:462,0,1783
-20	31263342	rs6141781	C	T	631.14	PASS	AC=1;AF=0.50;AN=2;DB;DP=249;DS;Dels=0.05;HRun=0;HaplotypeScore=351.4617;MQ=60.00;MQ0=0;QD=2.53;SB=-207.08;VQSLOD=-0.7834;sumGLbyD=2.66	GT:AD:DP:GQ:PL	0/1:142,83:156:99:661,0,1697
-20	31263507	rs6141782	A	G	373.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=247;DS;Dels=0.07;HRun=1;HaplotypeScore=526.3847;MQ=60.00;MQ0=0;QD=1.51;SB=-120.72;VQSLOD=-1.0972;sumGLbyD=1.63	GT:AD:DP:GQ:PL	0/1:161,60:153:99:404,0,2258
-20	31263609	.	T	C	855.51	PASS	AC=1;AF=0.50;AN=2;DP=243;DS;Dels=0.05;HRun=0;HaplotypeScore=276.0506;MQ=60.00;MQ0=0;QD=3.52;SB=-331.86;VQSLOD=-0.3909;sumGLbyD=3.64	GT:AD:DP:GQ:PL	0/1:146,84:166:99:886,0,1941
-20	31263802	rs6119932	G	T	411.50	PASS	AC=1;AF=0.50;AN=2;DB;DP=194;DS;Dels=0.03;HRun=0;HaplotypeScore=259.3848;MQ=60.00;MQ0=0;QD=2.12;SB=-98.14;VQSLOD=-0.7973;sumGLbyD=2.28	GT:AD:DP:GQ:PL	0/1:115,62:103:99:441,0,1210
-20	31264083	rs6057618	A	G	166.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=71;DS;Dels=0.10;HRun=1;HaplotypeScore=167.6891;MQ=60.00;MQ0=0;QD=2.35;SB=3.78;VQSLOD=-2.4185;sumGLbyD=2.77	GT:AD:DP:GQ:PL	0/1:43,19:48:99:197,0,645
-20	37989844	rs12625021	A	T	1329.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=226;Dels=0.02;HRun=0;HaplotypeScore=266.4430;MQ=60.00;MQ0=0;QD=5.88;SB=-610.01;VQSLOD=-2.3027;sumGLbyD=6.02	GT:AD:DP:GQ:PL	0/1:121,90:181:99:1360,0,1921
-20	37990272	rs1534975	G	T	908.18	PASS	AC=1;AF=0.50;AN=2;DB;DP=214;DS;Dels=0.11;HRun=1;HaplotypeScore=441.0712;MQ=60.00;MQ0=0;QD=4.24;SB=-416.07;VQSLOD=-1.5946;sumGLbyD=4.38	GT:AD:DP:GQ:PL	0/1:108,71:147:99:938,0,1549
-20	41227116	rs6093689	T	C	804.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=157;Dels=0.00;HRun=0;HaplotypeScore=141.8273;MQ=60.00;MQ0=0;QD=5.13;SB=-120.48;VQSLOD=-1.0587;sumGLbyD=5.32	GT:AD:DP:GQ:PL	0/1:90,59:114:99:835,0,1184
-20	41227405	rs6093690	A	C	754.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=246;DS;Dels=0.15;HRun=1;HaplotypeScore=633.8004;MQ=60.00;MQ0=0;QD=3.07;SB=-332.46;VQSLOD=-1.3684;sumGLbyD=3.19	GT:AD:DP:GQ:PL	0/1:139,66:175:99:785,0,2209
-20	41227521	rs6093691	G	C	1151.34	PASS	AC=1;AF=0.50;AN=2;DB;DP=248;DS;Dels=0.04;HRun=0;HaplotypeScore=354.5132;MQ=60.00;MQ0=0;QD=4.64;SB=-483.95;VQSLOD=-0.6231;sumGLbyD=4.76	GT:AD:DP:GQ:PL	0/1:137,90:184:99:1181,0,2024
-20	41227725	rs6102924	C	T	849.70	PASS	AC=1;AF=0.50;AN=2;DB;DP=208;DS;Dels=0.09;HRun=0;HaplotypeScore=370.4102;MQ=60.00;MQ0=0;QD=4.09;SB=-332.88;VQSLOD=-0.6667;sumGLbyD=4.23	GT:AD:DP:GQ:PL	0/1:112,75:123:99:880,0,1215
-20	41228178	rs6102925	A	G	168.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;DS;Dels=0.18;HRun=2;HaplotypeScore=317.8016;MQ=60.00;MQ0=0;QD=1.67;SB=-94.55;VQSLOD=-2.0738;sumGLbyD=1.97	GT:AD:DP:GQ:PL	0/1:54,26:51:99:199,0,710
-20	41258896	rs6016854	C	T	320.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=59;Dels=0.00;HRun=0;HaplotypeScore=58.0078;MQ=60.00;MQ0=0;QD=5.43;SB=-127.93;VQSLOD=-1.3142;sumGLbyD=5.94	GT:AD:DP:GQ:PL	0/1:31,28:36:99:350,0,292
-20	41259396	rs6030384	G	A	35.66	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.15;HRun=1;HaplotypeScore=72.1870;MQ=60.00;MQ0=0;QD=1.32;SB=-18.26;VQSLOD=-2.9758;sumGLbyD=2.43	GT:AD:DP:GQ:PL	0/1:14,8:16:65.65:66,0,162
-20	41733923	rs6513824	G	A	168.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;Dels=0.00;HRun=0;HaplotypeScore=80.2633;MQ=60.00;MQ0=0;QD=2.35;SB=-92.50;VQSLOD=-1.1311;sumGLbyD=2.76	GT:AD:DP:GQ:PL	0/1:50,21:39:99:199,0,435
-20	41734303	rs3091878	A	G	597.53	PASS	AC=1;AF=0.50;AN=2;DB;DP=191;Dels=0.00;HRun=0;HaplotypeScore=183.7429;MQ=60.00;MQ0=0;QD=3.13;SB=-263.06;VQSLOD=-0.2560;sumGLbyD=3.29	GT:AD:DP:GQ:PL	0/1:124,62:134:99:628,0,1587
-20	41734588	rs2425599	C	A	858.25	PASS	AC=1;AF=0.50;AN=2;DB;DP=233;Dels=0.08;HRun=1;HaplotypeScore=430.4773;MQ=60.00;MQ0=0;QD=3.68;SB=-335.59;VQSLOD=-1.4621;sumGLbyD=3.81	GT:AD:DP:GQ:PL	0/1:128,71:156:99:888,0,1737
-20	41734761	rs6016958	A	G	504.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=200;Dels=0.11;HRun=1;HaplotypeScore=438.6732;MQ=60.00;MQ0=0;QD=2.52;SB=-232.42;VQSLOD=-1.1738;sumGLbyD=2.67	GT:AD:DP:GQ:PL	0/1:101,71:116:99:534,0,1342
-20	42675942	.	C	A	116.43	PASS	AC=1;AF=0.50;AN=2;DP=28;Dels=0.00;HRun=0;HaplotypeScore=22.8089;MQ=60.00;MQ0=0;QD=4.16;SB=-11.79;VQSLOD=-2.2708;sumGLbyD=5.23	GT:AD:DP:GQ:PL	0/1:15,13:21:99:146,0,202
-20	44145615	rs6032263	T	C	133.01	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=40.1154;MQ=60.00;MQ0=0;QD=2.46;SB=-76.67;VQSLOD=-1.6117;sumGLbyD=3.02	GT:AD:DP:GQ:PL	0/1:40,14:33:99:163,0,389
-20	44145699	rs6032264	G	T	228.79	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.06;HRun=1;HaplotypeScore=126.2273;MQ=60.00;MQ0=0;QD=2.97;SB=-83.03;VQSLOD=-1.7897;sumGLbyD=3.36	GT:AD:DP:GQ:PL	0/1:46,25:55:99:259,0,549
-20	44145855	rs6032265	C	T	264.15	PASS	AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.30;HRun=1;HaplotypeScore=524.5167;MQ=60.00;MQ0=0;QD=2.11;SB=-111.49;VQSLOD=-1.1086;sumGLbyD=2.35	GT:AD:DP:GQ:PL	0/1:53,30:68:99:294,0,852
-20	44185086	rs6032311	C	T	171.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=54;Dels=0.00;HRun=0;HaplotypeScore=46.6061;MQ=60.00;MQ0=0;QD=3.18;SB=-75.60;VQSLOD=-1.2851;sumGLbyD=3.74	GT:AD:DP:GQ:PL	0/1:31,19:44:99:202,0,546
-20	44185127	rs6032312	C	G	268.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=66;Dels=0.06;HRun=0;HaplotypeScore=94.1521;MQ=60.00;MQ0=0;QD=4.07;SB=-67.66;VQSLOD=-1.0759;sumGLbyD=4.52	GT:AD:DP:GQ:PL	0/1:34,26:50:99:299,0,562
-20	44185198	rs8121615	T	C	290.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=84;Dels=0.10;HRun=1;HaplotypeScore=178.2142;MQ=60.00;MQ0=0;QD=3.46;SB=-112.62;VQSLOD=-1.3803;sumGLbyD=3.82	GT:AD:DP:GQ:PL	0/1:42,31:64:99:321,0,734
-20	44185231	rs62205620	G	A	534.44	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.07;HRun=1;HaplotypeScore=122.0246;MQ=60.00;MQ0=0;QD=6.14;SB=-144.94;VQSLOD=-1.1945;sumGLbyD=6.49	GT:AD:DP:GQ:PL	0/1:43,34:67:99:564,0,569
-20	44185259	rs62205621	C	T	489.99	PASS	AC=1;AF=0.50;AN=2;DB;DP=87;Dels=0.11;HRun=0;HaplotypeScore=187.5253;MQ=60.00;MQ0=0;QD=5.63;SB=-131.70;VQSLOD=-1.2624;sumGLbyD=5.98	GT:AD:DP:GQ:PL	0/1:42,33:67:99:520,0,662
-20	44185487	rs2868304	A	G	500.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=151;Dels=0.00;HRun=0;HaplotypeScore=123.8080;MQ=60.00;MQ0=0;QD=3.31;SB=-191.48;VQSLOD=-0.2646;sumGLbyD=3.51	GT:AD:DP:GQ:PL	0/1:93,50:109:99:530,0,1318
-20	44185500	rs6073781	T	C	603.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=155;Dels=0.00;HRun=0;HaplotypeScore=158.5440;MQ=60.00;MQ0=0;QD=3.89;SB=-217.88;VQSLOD=-0.1995;sumGLbyD=4.09	GT:AD:DP:GQ:PL	0/1:99,49:112:99:633,0,1340
-20	44185545	rs6017612	A	C	826.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=181;Dels=0.02;HRun=0;HaplotypeScore=306.6693;MQ=60.00;MQ0=0;QD=4.56;SB=-175.92;VQSLOD=-1.4629;sumGLbyD=4.73	GT:AD:DP:GQ:PL	0/1:108,68:130:99:856,0,1353
-20	44185556	rs6017613	A	G	413.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=193;Dels=0.01;HRun=0;HaplotypeScore=190.6336;MQ=60.00;MQ0=0;QD=2.14;SB=-22.78;VQSLOD=-1.2131;sumGLbyD=2.30	GT:AD:DP:GQ:PL	0/1:144,46:114:99:443,0,1448
-20	44185793	rs6032313	G	T	894.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=221;DS;Dels=0.18;HRun=1;HaplotypeScore=611.2823;MQ=60.00;MQ0=0;QD=4.05;SB=-394.87;VQSLOD=-1.6043;sumGLbyD=4.18	GT:AD:DP:GQ:PL	0/1:116,65:133:99:925,0,1403
-20	44185809	rs6017614	C	T	740.09	PASS	AC=1;AF=0.50;AN=2;DB;DP=223;DS;Dels=0.08;HRun=0;HaplotypeScore=365.7833;MQ=60.00;MQ0=0;QD=3.32;SB=-384.12;VQSLOD=-0.6293;sumGLbyD=3.45	GT:AD:DP:GQ:PL	0/1:120,74:153:99:770,0,1912
-20	44186027	rs62205622	G	A	669.55	PASS	AC=1;AF=0.50;AN=2;DB;DP=212;DS;Dels=0.00;HRun=0;HaplotypeScore=132.5166;MQ=60.00;MQ0=0;QD=3.16;SB=-347.96;VQSLOD=-0.8026;sumGLbyD=3.30	GT:AD:DP:GQ:PL	0/1:119,73:121:99:700,0,1248
-20	44186078	rs6017615	T	G	295.28	PASS	AC=1;AF=0.50;AN=2;DB;DP=184;DS;Dels=0.01;HRun=0;HaplotypeScore=229.5434;MQ=60.00;MQ0=0;QD=1.60;SB=-56.32;VQSLOD=-1.0986;sumGLbyD=1.77	GT:AD:DP:GQ:PL	0/1:141,41:87:99:325,0,1074
-20	44186147	rs6032314	T	C	633.96	PASS	AC=1;AF=0.50;AN=2;DB;DP=152;DS;Dels=0.03;HRun=0;HaplotypeScore=172.3554;MQ=60.00;MQ0=0;QD=4.17;SB=-285.13;VQSLOD=-0.3778;sumGLbyD=4.37	GT:AD:DP:GQ:PL	0/1:87,56:99:99:664,0,1024
-20	44186271	rs6032315	T	C	402.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=113;DS;Dels=0.13;HRun=1;HaplotypeScore=305.4757;MQ=60.00;MQ0=0;QD=3.56;SB=-206.41;VQSLOD=-1.3874;sumGLbyD=3.83	GT:AD:DP:GQ:PL	0/1:53,41:70:99:433,0,711
-20	44186287	rs6032316	G	A	565.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=112;DS;Dels=0.01;HRun=0;HaplotypeScore=114.6989;MQ=60.00;MQ0=0;QD=5.05;SB=-267.81;VQSLOD=-0.7667;sumGLbyD=5.31	GT:AD:DP:GQ:PL	0/1:53,55:67:99:595,0,572
-20	44186387	rs6104218	A	G	312.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=100;DS;Dels=0.06;HRun=0;HaplotypeScore=158.1833;MQ=60.00;MQ0=0;QD=3.12;SB=-125.91;VQSLOD=-0.3217;sumGLbyD=3.42	GT:AD:DP:GQ:PL	0/1:54,35:60:99:342,0,652
-20	44186427	rs62205623	G	A	263.80	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;DS;Dels=0.11;HRun=0;HaplotypeScore=222.1170;MQ=60.00;MQ0=0;QD=2.59;SB=-138.42;VQSLOD=-0.3799;sumGLbyD=2.88	GT:AD:DP:GQ:PL	0/1:55,30:50:99:294,0,434
-20	44247986	rs1487327	T	C	639.02	PASS	AC=1;AF=0.50;AN=2;DB;DP=88;Dels=0.01;HRun=0;HaplotypeScore=86.3576;MQ=60.00;MQ0=0;QD=7.26;SB=-189.61;VQSLOD=-1.0734;sumGLbyD=7.60	GT:AD:DP:GQ:PL	0/1:37,46:62:99:669,0,429
-20	44248055	rs1487326	T	C	519.98	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.13;HRun=1;HaplotypeScore=208.4444;MQ=60.00;MQ0=0;QD=5.59;SB=-107.88;VQSLOD=-1.2105;sumGLbyD=5.91	GT:AD:DP:GQ:PL	0/1:46,32:60:99:550,0,512
-20	44248435	rs3092045	G	A	662.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=183;Dels=0.08;HRun=0;HaplotypeScore=357.2661;MQ=60.00;MQ0=0;QD=3.62;SB=-334.51;VQSLOD=-0.5800;sumGLbyD=3.79	GT:AD:DP:GQ:PL	0/1:110,55:114:99:693,0,1083
-20	44248596	rs7509607	C	T	442.78	PASS	AC=1;AF=0.50;AN=2;DB;DP=165;Dels=0.07;HRun=0;HaplotypeScore=344.6687;MQ=60.00;MQ0=0;QD=2.68;SB=-222.55;VQSLOD=-0.7665;sumGLbyD=2.87	GT:AD:DP:GQ:PL	0/1:98,47:110:99:473,0,1183
-20	44248711	rs2903789	G	A	391.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=134;Dels=0.01;HRun=0;HaplotypeScore=189.1805;MQ=60.00;MQ0=0;QD=2.92;SB=-158.83;VQSLOD=-0.2152;sumGLbyD=3.14	GT:AD:DP:GQ:PL	0/1:90,35:93:99:421,0,1057
-20	47132653	.	C	A	269.31	PASS	AC=1;AF=0.50;AN=2;DP=29;Dels=0.00;HRun=0;HaplotypeScore=19.2962;MQ=60.00;MQ0=0;QD=9.29;SB=-133.76;VQSLOD=-1.7309;sumGLbyD=10.32	GT:AD:DP:GQ:PL	0/1:6,22:18:18.24:299,0,18
-20	47249116	rs4487145	G	A	102.90	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.08;HRun=1;HaplotypeScore=45.0180;MQ=60.00;MQ0=0;QD=1.98;SB=-23.95;VQSLOD=-3.0059;sumGLbyD=2.56	GT:AD:DP:GQ:PL	0/1:32,13:38:99:133,0,404
-20	47249170	rs4487146	G	A	249.27	PASS	AC=1;AF=0.50;AN=2;DB;DP=63;Dels=0.05;HRun=0;HaplotypeScore=95.7712;MQ=60.00;MQ0=0;QD=3.96;SB=-136.12;VQSLOD=-0.5428;sumGLbyD=4.43	GT:AD:DP:GQ:PL	0/1:38,18:52:99:279,0,553
-20	47249189	rs4413212	T	C	1029.04	PASS	AC=2;AF=1.00;AN=2;DB;DP=72;Dels=0.01;HRun=0;HaplotypeScore=90.5588;MQ=60.00;MQ0=0;QD=14.29;SB=-203.07;VQSLOD=-6.1490;sumGLbyD=14.75	GT:AD:DP:GQ:PL	1/1:7,56:49:99:1062,102,0
-20	47249200	rs4527260	A	G	219.64	PASS	AC=1;AF=0.50;AN=2;DB;DP=77;Dels=0.14;HRun=2;HaplotypeScore=216.0203;MQ=60.00;MQ0=0;QD=2.85;SB=-42.86;VQSLOD=-2.1207;sumGLbyD=3.24	GT:AD:DP:GQ:PL	0/1:40,19:54:99:250,0,686
-20	47249313	.	C	T	178.95	PASS	AC=1;AF=0.50;AN=2;DP=123;Dels=0.00;HRun=0;HaplotypeScore=113.8307;MQ=60.00;MQ0=0;QD=1.45;SB=-84.33;VQSLOD=-1.4563;sumGLbyD=1.70	GT:AD:DP:GQ:PL	0/1:87,28:72:99:209,0,848
-20	47249455	rs4810845	T	G	496.75	PASS	AC=1;AF=0.50;AN=2;DB;DP=237;Dels=0.00;HRun=0;HaplotypeScore=189.3521;MQ=60.00;MQ0=0;QD=2.10;SB=-237.24;VQSLOD=-0.6214;sumGLbyD=2.22	GT:AD:DP:GQ:PL	0/1:166,63:175:99:527,0,2536
-20	47249545	.	C	T	998.09	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.00;HRun=0;HaplotypeScore=317.5039;MQ=60.00;MQ0=0;QD=3.99;SB=-296.02;VQSLOD=-0.6255;sumGLbyD=4.11	GT:AD:DP:GQ:PL	0/1:159,80:160:99:1028,0,1561
-20	47249591	rs4810846	T	C	2090.58	PASS	AC=2;AF=1.00;AN=2;DB;DP=244;DS;Dels=0.04;HRun=0;HaplotypeScore=364.6909;MQ=60.00;MQ0=0;QD=8.57;SB=-801.27;VQSLOD=-1.7529;sumGLbyD=8.70	GT:AD:DP:GQ:PL	1/1:29,175:116:99:2124,151,0
-20	47249594	rs4809713	A	G	1173.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=245;DS;Dels=0.02;HRun=0;HaplotypeScore=307.0099;MQ=60.00;MQ0=0;QD=4.79;SB=-367.14;VQSLOD=-0.7244;sumGLbyD=4.91	GT:AD:DP:GQ:PL	0/1:137,94:189:99:1203,0,2026
-20	47249621	rs4809714	G	A	934.52	PASS	AC=1;AF=0.50;AN=2;DB;DP=250;DS;Dels=0.02;HRun=0;HaplotypeScore=376.9463;MQ=60.00;MQ0=0;QD=3.74;SB=-394.66;VQSLOD=-0.5067;sumGLbyD=3.86	GT:AD:DP:GQ:PL	0/1:152,83:185:99:965,0,1789
-20	47249705	rs4810847	C	T	722.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=248;DS;Dels=0.00;HRun=0;HaplotypeScore=272.4292;MQ=60.00;MQ0=0;QD=2.91;SB=-297.41;VQSLOD=-0.5081;sumGLbyD=3.03	GT:AD:DP:GQ:PL	0/1:151,83:134:99:753,0,1234
-20	47249921	rs4239656	C	T	2646.20	PASS	AC=2;AF=1.00;AN=2;DB;DP=220;DS;Dels=0.04;HRun=0;HaplotypeScore=292.2205;MQ=60.00;MQ0=0;QD=12.03;SB=-1272.34;VQSLOD=-10.3145;sumGLbyD=12.18	GT:AD:DP:GQ:PL	1/1:23,180:133:99:2679,161,0
-20	47249939	rs4128336	G	T	660.85	PASS	AC=1;AF=0.50;AN=2;DB;DP=224;DS;Dels=0.03;HRun=1;HaplotypeScore=236.3717;MQ=60.00;MQ0=0;QD=2.95;SB=-320.86;VQSLOD=-1.6409;sumGLbyD=3.08	GT:AD:DP:GQ:PL	0/1:140,73:170:99:691,0,2165
-20	47249963	rs58400536	A	G	936.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=229;DS;Dels=0.00;HRun=0;HaplotypeScore=162.0441;MQ=60.00;MQ0=0;QD=4.09;SB=-322.46;VQSLOD=-0.4951;sumGLbyD=4.22	GT:AD:DP:GQ:PL	0/1:126,88:145:99:966,0,1493
-20	47250115	rs4128342	A	G	325.17	PASS	AC=1;AF=0.50;AN=2;DB;DP=216;DS;Dels=0.16;HRun=2;HaplotypeScore=675.3933;MQ=60.00;MQ0=0;QD=1.51;SB=-146.07;VQSLOD=-2.4382;sumGLbyD=1.64	GT:AD:DP:GQ:PL	0/1:121,50:119:99:355,0,1623
-20	47250228	rs6019327	T	C	1372.60	PASS	AC=1;AF=0.50;AN=2;DB;DP=172;DS;Dels=0.00;HRun=0;HaplotypeScore=124.9500;MQ=60.00;MQ0=0;QD=7.98;SB=-463.91;VQSLOD=-1.4569;sumGLbyD=8.15	GT:AD:DP:GQ:PL	0/1:63,105:100:99:1403,0,341
-20	47250525	rs6125408	T	C	117.37	PASS	AC=1;AF=0.50;AN=2;DB;DP=72;DS;Dels=0.13;HRun=0;HaplotypeScore=174.4409;MQ=60.00;MQ0=0;QD=1.63;SB=-47.19;VQSLOD=-1.1854;sumGLbyD=2.05	GT:AD:DP:GQ:PL	0/1:33,28:22:99:147,0,208
-20	49133994	rs6067473	C	T	1012.32	PASS	AC=1;AF=0.50;AN=2;DB;DP=249;DS;Dels=0.07;HRun=1;HaplotypeScore=439.4730;MQ=60.00;MQ0=0;QD=4.07;SB=-427.89;VQSLOD=-1.6361;sumGLbyD=4.19	GT:AD:DP:GQ:PL	0/1:128,99:183:99:1042,0,2011
-20	49134099	rs6091173	C	T	561.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=247;DS;Dels=0.15;HRun=0;HaplotypeScore=768.9147;MQ=60.00;MQ0=0;QD=2.27;SB=-280.88;VQSLOD=-2.4780;sumGLbyD=2.40	GT:AD:DP:GQ:PL	0/1:141,66:135:99:592,0,1659
-20	49134535	rs13045492	A	T	223.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=89;DS;Dels=0.09;HRun=1;HaplotypeScore=149.5151;MQ=60.00;MQ0=0;QD=2.51;SB=-14.11;VQSLOD=-2.2943;sumGLbyD=2.85	GT:AD:DP:GQ:PL	0/1:51,29:53:99:254,0,682
-20	52476025	rs6022806	G	C	501.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=247;DS;Dels=0.08;HRun=0;HaplotypeScore=399.6134;MQ=60.00;MQ0=0;QD=2.03;SB=-208.89;VQSLOD=-0.8831;sumGLbyD=2.15	GT:AD:DP:GQ:PL	0/1:160,53:168:99:532,0,2316
-20	52476072	rs62206591	G	T	395.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=249;DS;Dels=0.04;HRun=1;HaplotypeScore=300.4377;MQ=60.00;MQ0=0;QD=1.59;SB=-91.93;VQSLOD=-1.7845;sumGLbyD=1.71	GT:AD:DP:GQ:PL	0/1:182,56:187:99:425,0,2381
-20	52476090	rs62206592	G	A	359	PASS	AC=1;AF=0.50;AN=2;DB;DP=248;DS;Dels=0.00;HRun=1;HaplotypeScore=201.9924;MQ=60.00;MQ0=0;QD=1.45;SB=-63.34;VQSLOD=-1.9362;sumGLbyD=1.57	GT:AD:DP:GQ:PL	0/1:189,57:163:99:389,0,2428
-20	52476103	.	T	A	99.08	PASS	AC=1;AF=0.50;AN=2;DP=245;DS;Dels=0.22;HRun=0;HaplotypeScore=812.4436;MQ=60.00;MQ0=0;QD=0.40;SB=24.97;VQSLOD=-5.4490;sumGLbyD=0.53	GT:AD:DP:GQ:PL	0/1:157,27:116:99:129,0,1767
-20	52476179	.	G	A	289.78	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.12;HRun=0;HaplotypeScore=598.6334;MQ=60.00;MQ0=0;QD=1.16;SB=49.48;VQSLOD=-4.6673;sumGLbyD=1.28	GT:AD:DP:GQ:PL	0/1:157,59:139:99:320,0,1794
-20	52476254	.	T	G	644.77	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.08;HRun=1;HaplotypeScore=403.8355;MQ=60.00;MQ0=0;QD=2.58;SB=-164.84;VQSLOD=-1.0674;sumGLbyD=2.70	GT:AD:DP:GQ:PL	0/1:163,64:189:99:675,0,2664
-20	52476280	.	T	G	415.96	PASS	AC=1;AF=0.50;AN=2;DP=248;DS;Dels=0.09;HRun=1;HaplotypeScore=555.5962;MQ=60.00;MQ0=0;QD=1.68;SB=-77.93;VQSLOD=-1.3816;sumGLbyD=1.80	GT:AD:DP:GQ:PL	0/1:174,44:176:99:446,0,2594
-20	52476292	.	A	G	202.93	PASS	AC=1;AF=0.50;AN=2;DP=249;DS;Dels=0.00;HRun=1;HaplotypeScore=247.6793;MQ=60.00;MQ0=0;QD=0.81;SB=-75.64;VQSLOD=-2.1649;sumGLbyD=0.94	GT:AD:DP:GQ:PL	0/1:203,45:162:99:233,0,2561
-20	52476310	.	T	C	630.63	PASS	AC=1;AF=0.50;AN=2;DP=248;DS;Dels=0.03;HRun=0;HaplotypeScore=284.7039;MQ=60.00;MQ0=0;QD=2.54;SB=-73.96;VQSLOD=-1.1267;sumGLbyD=2.66	GT:AD:DP:GQ:PL	0/1:167,64:182:99:661,0,2550
-20	52476314	.	A	G	354.19	PASS	AC=1;AF=0.50;AN=2;DP=248;DS;Dels=0.03;HRun=0;HaplotypeScore=278.2056;MQ=60.00;MQ0=0;QD=1.43;SB=-108.98;VQSLOD=-1.0228;sumGLbyD=1.55	GT:AD:DP:GQ:PL	0/1:173,63:181:99:384,0,2653
-20	52476337	.	C	T	628.48	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.04;HRun=0;HaplotypeScore=379.7543;MQ=60.00;MQ0=0;QD=2.51;SB=-181.62;VQSLOD=-0.8802;sumGLbyD=2.63	GT:AD:DP:GQ:PL	0/1:166,68:169:99:658,0,1887
-20	52476345	.	T	C	501.85	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.04;HRun=0;HaplotypeScore=411.6009;MQ=60.00;MQ0=0;QD=2.01;SB=-213.32;VQSLOD=-0.9158;sumGLbyD=2.13	GT:AD:DP:GQ:PL	0/1:175,61:165:99:532,0,2239
-20	52476360	.	T	C	356.05	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.08;HRun=1;HaplotypeScore=503.5609;MQ=60.00;MQ0=0;QD=1.42;SB=-156.60;VQSLOD=-1.0675;sumGLbyD=1.54	GT:AD:DP:GQ:PL	0/1:169,57:173:99:386,0,2548
-20	52476391	.	A	C	458.28	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.08;HRun=0;HaplotypeScore=514.0294;MQ=60.00;MQ0=0;QD=1.83;SB=-133.49;VQSLOD=-1.3976;sumGLbyD=1.95	GT:AD:DP:GQ:PL	0/1:155,74:155:99:488,0,2174
-20	52476410	.	G	A	763.43	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.04;HRun=0;HaplotypeScore=295.0130;MQ=60.00;MQ0=0;QD=3.05;SB=-279.14;VQSLOD=-0.5302;sumGLbyD=3.17	GT:AD:DP:GQ:PL	0/1:157,77:185:99:793,0,1998
-20	52476492	.	G	A	510.75	PASS	AC=1;AF=0.50;AN=2;DP=250;DS;Dels=0.12;HRun=0;HaplotypeScore=622.2692;MQ=60.00;MQ0=0;QD=2.04;SB=-251.28;VQSLOD=-2.0737;sumGLbyD=2.16	GT:AD:DP:GQ:PL	0/1:155,56:157:99:541,0,1724
-20	52476574	.	T	C	336.32	PASS	AC=1;AF=0.50;AN=2;DP=246;DS;Dels=0.00;HRun=0;HaplotypeScore=246.2194;MQ=60.00;MQ0=0;QD=1.37;SB=-172.93;VQSLOD=-0.8959;sumGLbyD=1.49	GT:AD:DP:GQ:PL	0/1:176,57:134:99:366,0,1867
-20	52476575	.	G	A	370.88	PASS	AC=1;AF=0.50;AN=2;DP=246;DS;Dels=0.06;HRun=0;HaplotypeScore=366.1878;MQ=60.00;MQ0=0;QD=1.51;SB=-188.29;VQSLOD=-1.0034;sumGLbyD=1.63	GT:AD:DP:GQ:PL	0/1:156,66:136:99:401,0,1932
-20	52476625	.	A	T	869.48	PASS	AC=1;AF=0.50;AN=2;DP=223;DS;Dels=0.00;HRun=0;HaplotypeScore=218.3572;MQ=60.00;MQ0=0;QD=3.90;SB=-414.92;VQSLOD=-0.5727;sumGLbyD=4.03	GT:AD:DP:GQ:PL	0/1:143,70:163:99:899,0,1867
-20	52476687	.	T	C	391.49	PASS	AC=1;AF=0.50;AN=2;DP=229;DS;Dels=0.07;HRun=0;HaplotypeScore=386.9302;MQ=60.00;MQ0=0;QD=1.71;SB=-193.53;VQSLOD=-0.9315;sumGLbyD=1.84	GT:AD:DP:GQ:PL	0/1:138,66:155:99:421,0,2096
-20	52476777	.	C	T	418.61	PASS	AC=1;AF=0.50;AN=2;DP=225;DS;Dels=0.02;HRun=0;HaplotypeScore=204.3801;MQ=60.00;MQ0=0;QD=1.86;SB=-215.09;VQSLOD=-0.6710;sumGLbyD=1.99	GT:AD:DP:GQ:PL	0/1:150,66:155:99:449,0,1894
-20	52476821	.	T	A	47.11	PASS	AC=1;AF=0.50;AN=2;DP=208;DS;Dels=0.17;HRun=5;HaplotypeScore=559.6455;MQ=60.00;MQ0=0;QD=0.23;SB=12.85;VQSLOD=-11.3252;sumGLbyD=0.37	GT:AD:DP:GQ:PL	0/1:145,23:100:77.10:77,0,1576
-20	52476830	.	T	C	262.84	PASS	AC=1;AF=0.50;AN=2;DP=205;DS;Dels=0.12;HRun=1;HaplotypeScore=490.3966;MQ=60.00;MQ0=0;QD=1.28;SB=-142.88;VQSLOD=-1.1170;sumGLbyD=1.43	GT:AD:DP:GQ:PL	0/1:131,48:143:99:293,0,2184
-20	52476840	.	T	C	589.46	PASS	AC=1;AF=0.50;AN=2;DP=198;DS;Dels=0.01;HRun=0;HaplotypeScore=164.8113;MQ=60.00;MQ0=0;QD=2.98;SB=-257.78;VQSLOD=-0.3140;sumGLbyD=3.13	GT:AD:DP:GQ:PL	0/1:133,59:138:99:619,0,1733
-20	52476888	.	C	T	645.07	PASS	AC=1;AF=0.50;AN=2;DP=188;DS;Dels=0.00;HRun=0;HaplotypeScore=134.2804;MQ=60.00;MQ0=0;QD=3.43;SB=-335.89;VQSLOD=-0.6563;sumGLbyD=3.59	GT:AD:DP:GQ:PL	0/1:128,50:121:99:675,0,1451
-20	52476914	.	C	G	462	PASS	AC=1;AF=0.50;AN=2;DP=178;DS;Dels=0.02;HRun=0;HaplotypeScore=131.2548;MQ=60.00;MQ0=0;QD=2.60;SB=-161.08;VQSLOD=-0.4323;sumGLbyD=2.76	GT:AD:DP:GQ:PL	0/1:124,45:126:99:492,0,1696
-20	52476951	.	T	A	206.06	PASS	AC=1;AF=0.50;AN=2;DP=164;DS;Dels=0.03;HRun=0;HaplotypeScore=194.9711;MQ=60.00;MQ0=0;QD=1.26;SB=-104.40;VQSLOD=-1.0620;sumGLbyD=1.44	GT:AD:DP:GQ:PL	0/1:111,41:112:99:236,0,1806
-20	52476958	.	C	T	153.11	PASS	AC=1;AF=0.50;AN=2;DP=164;DS;Dels=0.09;HRun=1;HaplotypeScore=294.3348;MQ=60.00;MQ0=0;QD=0.93;SB=-28.07;VQSLOD=-2.4629;sumGLbyD=1.12	GT:AD:DP:GQ:PL	0/1:114,28:98:99:183,0,1329
-20	52476975	.	C	T	291.85	PASS	AC=1;AF=0.50;AN=2;DP=155;DS;Dels=0.00;HRun=0;HaplotypeScore=182.7610;MQ=60.00;MQ0=0;QD=1.88;SB=-56.75;VQSLOD=-0.9911;sumGLbyD=2.08	GT:AD:DP:GQ:PL	0/1:107,37:93:99:322,0,1071
-20	52476992	.	T	C	399.94	PASS	AC=1;AF=0.50;AN=2;DP=150;DS;Dels=0.02;HRun=0;HaplotypeScore=167.8167;MQ=60.00;MQ0=0;QD=2.67;SB=-117.76;VQSLOD=-0.4013;sumGLbyD=2.87	GT:AD:DP:GQ:PL	0/1:97,47:113:99:430,0,1463
-20	52477015	.	G	A	109.08	PASS	AC=1;AF=0.50;AN=2;DP=143;DS;Dels=0.06;HRun=1;HaplotypeScore=273.2263;MQ=60.00;MQ0=0;QD=0.76;SB=-7.20;VQSLOD=-2.6386;sumGLbyD=0.97	GT:AD:DP:GQ:PL	0/1:96,38:91:99:139,0,1203
-20	52477026	.	A	T	292.55	PASS	AC=1;AF=0.50;AN=2;DP=144;DS;Dels=0.05;HRun=2;HaplotypeScore=225.5374;MQ=60.00;MQ0=0;QD=2.03;SB=-47.13;VQSLOD=-2.1255;sumGLbyD=2.24	GT:AD:DP:GQ:PL	0/1:92,39:92:99:323,0,1293
-20	52477058	.	G	A	562.78	PASS	AC=1;AF=0.50;AN=2;DP=136;DS;Dels=0.02;HRun=0;HaplotypeScore=142.1341;MQ=60.00;MQ0=0;QD=4.14;SB=-204.35;VQSLOD=-0.2761;sumGLbyD=4.36	GT:AD:DP:GQ:PL	0/1:88,44:106:99:593,0,1304
-20	52477066	.	T	C	173.83	PASS	AC=1;AF=0.50;AN=2;DP=137;DS;Dels=0.00;HRun=0;HaplotypeScore=82.8043;MQ=60.00;MQ0=0;QD=1.27;SB=-66.19;VQSLOD=-1.9920;sumGLbyD=1.49	GT:AD:DP:GQ:PL	0/1:104,30:90:99:204,0,1317
-20	52477120	.	G	T	364.17	PASS	AC=1;AF=0.50;AN=2;DP=128;DS;Dels=0.03;HRun=0;HaplotypeScore=111.3768;MQ=60.00;MQ0=0;QD=2.85;SB=-43.39;VQSLOD=-1.0840;sumGLbyD=3.08	GT:AD:DP:GQ:PL	0/1:86,36:88:99:394,0,1159
-20	52477162	.	A	G	231.10	PASS	AC=1;AF=0.50;AN=2;DP=122;DS;Dels=0.11;HRun=1;HaplotypeScore=301.7020;MQ=60.00;MQ0=0;QD=1.89;SB=-111.39;VQSLOD=-1.5861;sumGLbyD=2.14	GT:AD:DP:GQ:PL	0/1:77,28:72:99:261,0,972
-20	52477216	rs56158048	C	G	120.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=107;DS;Dels=0.03;HRun=0;HaplotypeScore=206.1839;MQ=60.00;MQ0=0;QD=1.13;SB=-38.53;VQSLOD=-1.3969;sumGLbyD=1.41	GT:AD:DP:GQ:PL	0/1:74,27:61:99:151,0,926
-20	52477243	.	G	A	129.98	PASS	AC=1;AF=0.50;AN=2;DP=105;DS;Dels=0.07;HRun=1;HaplotypeScore=182.7841;MQ=60.00;MQ0=0;QD=1.24;SB=-58.90;VQSLOD=-2.0782;sumGLbyD=1.52	GT:AD:DP:GQ:PL	0/1:72,24:55:99:160,0,805
-20	52477258	.	C	T	133.06	PASS	AC=1;AF=0.50;AN=2;DP=102;DS;Dels=0.07;HRun=1;HaplotypeScore=145.0557;MQ=60.00;MQ0=0;QD=1.30;SB=-61.24;VQSLOD=-2.1698;sumGLbyD=1.60	GT:AD:DP:GQ:PL	0/1:59,35:56:99:163,0,791
-20	52477282	.	G	A	56.71	PASS	AC=1;AF=0.50;AN=2;DP=94;DS;Dels=0.18;HRun=0;HaplotypeScore=332.8721;MQ=60.00;MQ0=0;QD=0.60;SB=-29.83;VQSLOD=-1.8082;sumGLbyD=0.92	GT:AD:DP:GQ:PL	0/1:47,26:40:86.70:87,0,470
-20	52477289	.	C	T	105	PASS	AC=1;AF=0.50;AN=2;DP=93;DS;Dels=0.15;HRun=1;HaplotypeScore=235.1778;MQ=60.00;MQ0=0;QD=1.13;SB=-49.61;VQSLOD=-2.1302;sumGLbyD=1.45	GT:AD:DP:GQ:PL	0/1:51,25:42:99:135,0,587
-20	56523601	rs6025925	G	C	148.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.03;HRun=0;HaplotypeScore=30.0349;MQ=60.00;MQ0=0;QD=4.65;SB=-87.54;VQSLOD=-1.5376;sumGLbyD=5.58	GT:AD:DP:GQ:PL	0/1:18,13:27:99:179,0,300
-20	56523643	rs6025926	T	C	134.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=43;Dels=0.00;HRun=0;HaplotypeScore=53.9853;MQ=60.00;MQ0=0;QD=3.13;SB=-35.08;VQSLOD=-1.5668;sumGLbyD=3.83	GT:AD:DP:GQ:PL	0/1:26,15:30:99:165,0,339
-20	56523799	rs6025927	T	C	155.42	PASS	AC=1;AF=0.50;AN=2;DB;DP=52;Dels=0.04;HRun=0;HaplotypeScore=77.7376;MQ=60.00;MQ0=0;QD=2.99;SB=-47.18;VQSLOD=-1.2535;sumGLbyD=3.57	GT:AD:DP:GQ:PL	0/1:26,22:31:99:185,0,361
-20	56524660	rs59556206	C	T	33.82	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.00;HRun=0;HaplotypeScore=38.6534;MQ=60.00;MQ0=0;QD=1.21;SB=-26.41;VQSLOD=-2.8205;sumGLbyD=2.28	GT:AD:DP:GQ:PL	0/1:14,14:11:63.81:64,0,136
-20	57577935	rs163798	A	G	178.07	PASS	AC=1;AF=0.50;AN=2;DB;DP=40;Dels=0.08;HRun=0;HaplotypeScore=74.4582;MQ=60.00;MQ0=0;QD=4.45;SB=-103.21;VQSLOD=-1.0021;sumGLbyD=5.20	GT:AD:DP:GQ:PL	0/1:20,14:33:99:208,0,387
-20	57578420	rs56352943	A	G	552.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=123;Dels=0.00;HRun=0;HaplotypeScore=141.5473;MQ=60.00;MQ0=0;QD=4.50;SB=-253.33;VQSLOD=-0.4388;sumGLbyD=4.74	GT:AD:DP:GQ:PL	0/1:79,42:96:99:583,0,1028
-20	57578508	rs163800	T	C	1342.35	PASS	AC=2;AF=1.00;AN=2;DB;DP=122;Dels=0.04;HRun=0;HaplotypeScore=143.0812;MQ=60.00;MQ0=0;QD=11.00;SB=-641.51;VQSLOD=-1.6803;sumGLbyD=11.27	GT:AD:DP:GQ:PL	1/1:4,102:73:99:1375,207,0
-20	57578614	rs163801	A	G	1331.08	PASS	AC=2;AF=1.00;AN=2;DB;DP=127;Dels=0.20;HRun=1;HaplotypeScore=423.7909;MQ=60.00;MQ0=0;QD=10.48;SB=-576.57;VQSLOD=-1.9233;sumGLbyD=10.74	GT:AD:DP:GQ:PL	1/1:7,88:77:99:1364,134,0
-20	57578852	rs163802	C	G	76.71	PASS	AC=1;AF=0.50;AN=2;DB;DP=137;Dels=0.32;HRun=3;HaplotypeScore=664.1589;MQ=60.00;MQ0=0;QD=0.56;SB=1.54;VQSLOD=-5.5650;sumGLbyD=0.78	GT:AD:DP:GQ:PL	0/1:70,20:69:99:107,0,827
-20	58170882	rs2180680	G	A	590.19	PASS	AC=1;AF=0.50;AN=2;DB;DP=119;Dels=0.03;HRun=0;HaplotypeScore=118.1657;MQ=60.00;MQ0=0;QD=4.96;SB=-247.23;VQSLOD=-0.6701;sumGLbyD=5.21	GT:AD:DP:GQ:PL	0/1:64,49:97:99:620,0,890
-20	58170900	rs4812116	T	C	481.49	PASS	AC=1;AF=0.50;AN=2;DB;DP=125;Dels=0.02;HRun=0;HaplotypeScore=188.7468;MQ=60.00;MQ0=0;QD=3.85;SB=-152.37;VQSLOD=-0.3499;sumGLbyD=4.09	GT:AD:DP:GQ:PL	0/1:76,40:92:99:511,0,1002
-20	59455378	rs2016776	A	G	65.35	PASS	AC=1;AF=0.50;AN=2;DB;DP=20;Dels=0.00;HRun=0;HaplotypeScore=13.5277;MQ=60.00;MQ0=0;QD=3.27;SB=-31.46;VQSLOD=-2.0555;sumGLbyD=4.77	GT:AD:DP:GQ:PL	0/1:12,8:15:95.35:95,0,154
-20	59456370	rs6027899	T	C	125.23	PASS	AC=1;AF=0.50;AN=2;DB;DP=34;Dels=0.03;HRun=0;HaplotypeScore=34.9707;MQ=60.00;MQ0=0;QD=3.68;SB=-58.07;VQSLOD=-1.5221;sumGLbyD=4.57	GT:AD:DP:GQ:PL	0/1:15,16:23:99:155,0,223
-20	59456392	rs6027900	A	G	156.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=32;Dels=0.03;HRun=0;HaplotypeScore=33.6051;MQ=60.00;MQ0=0;QD=4.88;SB=-70.80;VQSLOD=-1.7700;sumGLbyD=5.81	GT:AD:DP:GQ:PL	0/1:19,12:19:99:186,0,148
-20	59456420	rs2426932	T	C	153.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.11;HRun=1;HaplotypeScore=71.3263;MQ=60.00;MQ0=0;QD=5.49;SB=-80.48;VQSLOD=-2.1741;sumGLbyD=6.57	GT:AD:DP:GQ:PL	0/1:11,12:13:13.64:184,0,14
-20	59456449	rs2426933	C	A	46.54	PASS	AC=1;AF=0.50;AN=2;DB;DP=27;Dels=0.00;HRun=1;HaplotypeScore=23.7046;MQ=60.00;MQ0=0;QD=1.72;SB=-8.75;VQSLOD=-3.4501;sumGLbyD=2.83	GT:AD:DP:GQ:PL	0/1:19,8:14:76.53:77,0,171
-20	60509879	rs4925318	A	G	160.16	PASS	AC=1;AF=0.50;AN=2;DB;DP=78;Dels=0.05;HRun=0;HaplotypeScore=142.3092;MQ=60.00;MQ0=0;QD=2.05;SB=-83.96;VQSLOD=-0.8706;sumGLbyD=2.44	GT:AD:DP:GQ:PL	0/1:46,27:50:99:190,0,597
-20	60509955	rs4925319	G	A	342.92	PASS	AC=1;AF=0.50;AN=2;DB;DP=85;Dels=0.01;HRun=0;HaplotypeScore=106.2051;MQ=60.00;MQ0=0;QD=4.03;SB=-121.59;VQSLOD=-0.5877;sumGLbyD=4.39	GT:AD:DP:GQ:PL	0/1:44,36:63:99:373,0,723
-20	60509995	rs4925320	C	A	279.93	PASS	AC=1;AF=0.50;AN=2;DB;DP=93;Dels=0.04;HRun=2;HaplotypeScore=135.2499;MQ=60.00;MQ0=0;QD=3.01;SB=-127.49;VQSLOD=-2.0055;sumGLbyD=3.33	GT:AD:DP:GQ:PL	0/1:50,36:60:99:310,0,707
-20	60510043	rs4925321	G	A	384.86	PASS	AC=1;AF=0.50;AN=2;DB;DP=101;Dels=0.03;HRun=0;HaplotypeScore=124.2625;MQ=60.00;MQ0=0;QD=3.81;SB=-186.91;VQSLOD=-0.2629;sumGLbyD=4.11	GT:AD:DP:GQ:PL	0/1:56,34:73:99:415,0,685
-20	60510337	rs2153936	C	T	628.21	PASS	AC=1;AF=0.50;AN=2;DB;DP=214;Dels=0.02;HRun=0;HaplotypeScore=247.2870;MQ=60.00;MQ0=0;QD=2.94;SB=-212.89;VQSLOD=-0.3082;sumGLbyD=3.08	GT:AD:DP:GQ:PL	0/1:123,73:152:99:658,0,1869
-20	60510417	rs6089559	C	T	778.08	PASS	AC=1;AF=0.50;AN=2;DB;DP=234;Dels=0.00;HRun=0;HaplotypeScore=244.9003;MQ=60.00;MQ0=0;QD=3.33;SB=-386.26;VQSLOD=-0.5199;sumGLbyD=3.45	GT:AD:DP:GQ:PL	0/1:143,81:135:99:808,0,1482
-20	60510422	rs2153935	A	C	620.76	PASS	AC=1;AF=0.50;AN=2;DB;DP=234;Dels=0.12;HRun=1;HaplotypeScore=607.6288;MQ=60.00;MQ0=0;QD=2.65;SB=-246.28;VQSLOD=-1.4133;sumGLbyD=2.78	GT:AD:DP:GQ:PL	0/1:133,62:163:99:651,0,1992
-20	60510750	rs6142885	A	C	2258.36	PASS	AC=2;AF=1.00;AN=2;DB;DP=190;Dels=0.09;HRun=1;HaplotypeScore=359.1129;MQ=60.00;MQ0=0;QD=11.89;SB=-1072.04;VQSLOD=-5.5742;sumGLbyD=12.06	GT:AD:DP:GQ:PL	1/1:8,150:108:99:2291,269,0
-20	61816492	rs6090278	C	T	224.05	PASS	AC=1;AF=0.50;AN=2;DB;DP=51;Dels=0.06;HRun=0;HaplotypeScore=79.7334;MQ=60.00;MQ0=0;QD=4.39;SB=-91.32;VQSLOD=-1.0462;sumGLbyD=4.98	GT:AD:DP:GQ:PL	0/1:24,21:36:99:254,0,327
-20	61816789	rs6090279	G	A	652.48	PASS	AC=1;AF=0.50;AN=2;DB;DP=159;Dels=0.05;HRun=0;HaplotypeScore=225.7796;MQ=60.00;MQ0=0;QD=4.10;SB=-320.92;VQSLOD=-0.4184;sumGLbyD=4.29	GT:AD:DP:GQ:PL	0/1:91,57:114:99:682,0,1042
-20	61816951	rs6090280	T	C	866.74	PASS	AC=1;AF=0.50;AN=2;DB;DP=212;Dels=0.06;HRun=0;HaplotypeScore=350.3056;MQ=60.00;MQ0=0;QD=4.09;SB=-225.82;VQSLOD=-1.2257;sumGLbyD=4.23	GT:AD:DP:GQ:PL	0/1:106,84:147:99:897,0,1528
-20	61817385	rs6089856	C	T	895.57	PASS	AC=1;AF=0.50;AN=2;DB;DP=170;Dels=0.04;HRun=0;HaplotypeScore=200.4081;MQ=60.00;MQ0=0;QD=5.27;SB=-440.80;VQSLOD=-1.1392;sumGLbyD=5.44	GT:AD:DP:GQ:PL	0/1:81,73:123:99:926,0,954
-20	61817589	rs6090281	C	T	390.59	PASS	AC=1;AF=0.50;AN=2;DB;DP=102;Dels=0.01;HRun=0;HaplotypeScore=87.2202;MQ=60.00;MQ0=0;QD=3.83;SB=-141.97;VQSLOD=-0.5485;sumGLbyD=4.12	GT:AD:DP:GQ:PL	0/1:59,42:63:99:421,0,602
-20	61967037	rs9680065	G	A	233.26	PASS	AC=1;AF=0.50;AN=2;DB;DP=107;Dels=0.08;HRun=1;HaplotypeScore=199.3982;MQ=60.00;MQ0=0;QD=2.18;SB=-129.21;VQSLOD=-1.4181;sumGLbyD=2.46	GT:AD:DP:GQ:PL	0/1:59,37:53:99:263,0,607
-20	61967440	rs6011759	C	G	133.02	PASS	AC=2;AF=1.00;AN=2;DB;DP=32;Dels=0.00;HRun=0;HaplotypeScore=86.7767;MQ=60.00;MQ0=0;QD=4.16;SB=-74.81;VQSLOD=-0.6803;sumGLbyD=5.19	GT:AD:DP:GQ:PL	1/1:8,23:8:23.74:166,24,0
-20	62388627	rs6089973	C	T	150.33	PASS	AC=1;AF=0.50;AN=2;DB;DP=28;Dels=0.07;HRun=1;HaplotypeScore=41.2425;MQ=60.00;MQ0=0;QD=5.37;SB=-53.10;VQSLOD=-2.9388;sumGLbyD=6.44	GT:AD:DP:GQ:PL	0/1:14,11:20:99:180,0,120
-20	62388655	rs6011086	C	T	272.91	PASS	AC=2;AF=1.00;AN=2;DB;DP=31;Dels=0.32;HRun=4;HaplotypeScore=103.6966;MQ=60.00;MQ0=0;QD=8.80;SB=-71.11;VQSLOD=-12.9297;sumGLbyD=9.87	GT:AD:DP:GQ:PL	1/1:2,17:15:21.18:306,21,0
-20	62388897	rs6010640	T	C	426.90	PASS	AC=2;AF=1.00;AN=2;DB;DP=55;Dels=0.13;HRun=0;HaplotypeScore=142.0259;MQ=60.00;MQ0=0;QD=7.76;SB=-188.69;VQSLOD=-0.8076;sumGLbyD=8.36	GT:AD:DP:GQ:PL	1/1:8,36:28:34.67:460,35,0

public/testdata/VariantEval/silent.txt

@@ -1 +0,0 @@
-20	10019093	rs575534	A	G	69795.04	PASS	AC=3;AF=0.50;AN=6;DBSNP129;DBSNP132;DP=14;OMNI;refseq.changesAA_1=false;refseq.changesAA_2=false;refseq.chr_1=20;refseq.chr_2=20;refseq.codingCoordStr_1=c.144A>G;refseq.codingCoordStr_2=c.144A>G;refseq.codonCoord_1=48;refseq.codonCoord_2=48;refseq.end_1=10019093;refseq.end_2=10019093;refseq.frame_1=2;refseq.frame_2=2;refseq.functionalClass_1=silent;refseq.functionalClass_2=silent;refseq.haplotypeAlternate_1=G;refseq.haplotypeAlternate_2=G;refseq.haplotypeReference_1=A;refseq.haplotypeReference_2=A;refseq.inCodingRegion_1=true;refseq.inCodingRegion_2=true;refseq.mrnaCoord_1=537;refseq.mrnaCoord_2=473;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.numMatchingRecords=2;refseq.positionType_1=CDS;refseq.positionType_2=CDS;refseq.proteinCoordStr_1=p.G48G;refseq.proteinCoordStr_2=p.G48G;refseq.referenceAA_1=Gly;refseq.referenceAA_2=Gly;refseq.referenceCodon_1=GGA;refseq.referenceCodon_2=GGA;refseq.spliceDist_1=188;refseq.spliceDist_2=188;refseq.start_1=10019093;refseq.start_2=10019093;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.variantAA_1=Gly;refseq.variantAA_2=Gly;refseq.variantCodon_1=GGG;refseq.variantCodon_2=GGG	GT:DP:GQ:PL	0/1:3:24:24,0,60	0/0:6:18:0,18,211	1/1:5:15:172,15,0

public/testdata/VariantEval/transition.vcf

@@ -1,3 +0,0 @@
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10003692	rs2064653	A	G	119873.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=9	GT:DP:GQ:PL	1/1:2:6:66,6,0	0/1:4:20:20,0,85	1/1:3:9:112,9,0

public/testdata/VariantEval/transversion.vcf

@@ -1,3 +0,0 @@
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625
-20	10003358	rs926982	A	C	92318.04	PASS	AC=5;AF=0.83;AN=6;DBSNP129;DBSNP132;DP=7	GT:DP:GQ:PL	1/1:1:3:34,3,0	0/1:5:51:51,0,95	1/1:1:3:27,3,0

public/testdata/allelesForUG.vcf

@@ -1,6 +0,0 @@
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA19240
-20	10000688	.	C	G	213.10	.	AC=1;AF=0.25;AN=4;DP=46;Dels=0.00;HRun=1;HaplotypeScore=4.8419;MQ=94.33;MQ0=0;QD=8.20;SB=-139.26;sumGLbyD=9.47	GT:AD:DP:GQ:PL	0/1:15,10:23:99:246,0,364	0/0:20,0:20:60.12:0,60,635
-20	10001023	.	T	A	291.78	.	AC=1;AF=0.25;AN=4;DP=70;Dels=0.00;HRun=0;HaplotypeScore=8.1219;MQ=90.98;MQ0=0;QD=10.81;SB=-108.18;sumGLbyD=12.03	GT:AD:DP:GQ:PL	0/0:42,0:35:99:0,102,1144	0/1:13,14:24:99:325,0,283
-20	10001267	.	G	A	202.35	.	AC=1;AF=0.25;AN=4;DP=69;Dels=0.00;HRun=0;HaplotypeScore=8.5086;MQ=88.37;MQ0=0;QD=6.98;SB=-92.88;sumGLbyD=8.12	GT:AD:DP:GQ:PL	0/0:40,0:31:93.20:0,93,983	0/1:17,12:25:99:235,0,371
-20	10001395	.	G	A	1022.27	.	AC=2;AF=0.50;AN=4;DP=82;Dels=0.00;HRun=0;HaplotypeScore=8.3689;MQ=90.24;MQ0=0;QD=23.77;SB=-409.81;sumGLbyD=24.72	GT:AD:DP:GQ:PL	0/0:35,0:29:87.23:0,87,972	1/1:0,43:36:99:1063,108,0

public/testdata/amplicon_interval_table1.table

@@ -1,6 +0,0 @@
-HEADERpos	name
-20:207334-207494	20_207414
-20:792042-792202	20_792122
-20:994065-994225	20_994145
-20:1074150-1074310	20_1074230
-20:1084250-1084410	20_1084330

public/testdata/amplicon_mask_sites.vcf

@@ -1,11 +0,0 @@
-##fileformat=VCFv4.1
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA1
-20	207414	.	G	A	77.12	PASS	.	GT	0/0
-20	207416	.	A	AGGC	49422.34	PASS	.	GT	0/0
-20	792076	.	A	G	2637.15	HaplotypeScore	.	GT	0/0
-20	792080	.	T	G	161.83	PASS	.	GT	0/0
-20	792087	.	CGGT	C	179.84	ReadPosRankSum	.	GT	0/0
-20	792106	.	C	G	32.59	PASS	.	GT	0/0
-20	792140	.	C	G	409.75	PASS	.	GT	0/0
-20	1084319	.	T	A,C	22.24	PASS	.	GT	0/0
-20	1084348	.	TACCACCCCACACA	T	482.84	PASS	.	GT	0/0

public/testdata/badIntervalLocations.list

@@ -1,2 +0,0 @@
-chr1:10-7
-chr1:1-5

public/testdata/breakpoint-example.vcf

@@ -1,8 +0,0 @@
-##fileformat=VCFv4.1
-##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SVTYPE">
-##INFO=<ID=MATEID,Number=1,Type=String,Description="MATEID">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-22	50	bnd_W	G	G]22:6000]	6	PASS	SVTYPE=BND;MATEID=bnd_Y
-22	51	bnd_V	T	]22:55]T	6	PASS	SVTYPE=BND;MATEID=bnd_U
-22	55	bnd_U	C	C[22:51[	6	PASS	SVTYPE=BND;MATEID=bnd_V
-22	6000	bnd_Y	A	A]22:50]	6	PASS	SVTYPE=BND;MATEID=bnd_W

public/testdata/ceutrio.ped

@@ -1,3 +0,0 @@
-fam1 kid dad mom 1 2
-fam1 dad 0   0   1 1
-fam1 mom 0   0   2 2

public/testdata/combine.1.vcf

@@ -1,10 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FILTER=<ID=FAIL,Description="Fail">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891
-20	9999996	.	A	ACT	.	PASS	.	GT:GQ	0/1:30
-20	10000000	.	T	G	.	PASS	.	GT:GQ	0/1:30
-20	10000117	.	C	T	.	FAIL	.	GT:GQ	0/1:30
-20	10000211	.	C	T	.	PASS	.	GT:GQ	0/1:30
-20	10001436	.	A	AGG	.	PASS	.	GT:GQ	1/1:30

public/testdata/combine.2.vcf

@@ -1,10 +0,0 @@
-##fileformat=VCFv4.0
-##FILTER=<ID=FAIL,Description="Didnt pass">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878
-20	9999996	.	A	ACT	.	PASS	.	GT:GQ	0/1:30
-20	10000117	.	C	T	.	FAIL	.	GT:GQ	0/1:30
-20	10000211	.	C	T	.	FAIL	.	GT:GQ	0/1:30
-20	10000598	.	T	A	.	PASS	.	GT:GQ	1/1:30
-20	10001436	.	A	AGGCT	.	PASS	.	GT:GQ	1/1:30

public/testdata/combine.3.vcf

@@ -1,7 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891	NA12892
-20	10000000	.	T	G	.	PASS	.	GT:PL	0/1:10,0,10	0/1:10,0,12
-20	10000117	.	C	T	.	PASS	.	GT:PL	0/1:10,0,10	0/0:0,10,80
-20	10000211	.	C	T	.	PASS	.	GT:PL	0/1:10,0,10	1/1:90,10,0

public/testdata/combine.4.vcf

@@ -1,7 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12893	NA12894
-20	10000000	.	T	A	.	PASS	.	GT:PL	0/1:10,0,10	0/1:10,0,12
-20	10000117	.	C	T	.	PASS	.	GT	0/1	0/0
-20	10000211	.	C	A	.	PASS	.	GT:PL	0/1:10,0,10	./.

public/testdata/combine.5.vcf

@@ -1,7 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891	NA12892
-20	10000000	.	T	G	.	PASS	.	GT:PL	0/1:10,0,10	0/1:10,0,12
-20	10000117	.	C	A,T	.	PASS	.	GT:PL	0/1:10,0,10	0/2:0,10,80
-20	10000211	.	C	T	.	PASS	.	GT:PL	0/1:10,0,10	1/1:90,10,0

public/testdata/combine.6.vcf

@@ -1,10 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12891	NA12892
-20	10000000	.	T	G	.	PASS	.	GT:PL	0/1:10,0,10	0/1:10,0,12
-20	10000117	.	C	A,T	.	PASS	.	GT:PL	0/1:10,0,10	0/2:0,10,80
-20	10000211	.	C	T	.	PASS	.	GT:PL	0/1:10,0,10	1/1:90,10,0
-20	10001436	.	A	AGG,T	.	PASS	.	GT:GQ	1/1:30
-

public/testdata/complexExample.vcf4

@@ -1,33 +0,0 @@
-##fileformat=VCFv4.0
-##source=ArbitrarySource
-##FILTER=<ID=foo,Description="foo">
-##FILTER=<ID=bar,Description="bar">
-##FILTER=<ID=baz,Description="baz">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##INFO=<ID=AlleleBalance,Number=A,Type=Float,Description="Allele balance">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=DoC,Number=1,Type=Integer,Description="Filtered Depth">
-##INFO=<ID=HomopolymerRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
-##INFO=<ID=NS,Number=1,Type=Float,Description="Number of samples">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=MAPQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=RMSMAPQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=SB,Number=1,Type=Float,Description="Strand bias">
-##INFO=<ID=SpanningDeletions,Number=1,Type=Integer,Description="No spanning deletions">
-##reference=human_b36_both.fasta
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-1	10001292	testid1	G	A	12.22	PASS	AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0	GT:DP:GQ	1/0:23:19.27	./.	./.
-1	10002963	.	C	G	22.22	.	AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0	GT:DP:GQ	0/1:30:33.07	./.	./.
-1	10005008	.	A	T,C	123.78	PASS	AF=1.00,0.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1	GT:DP:GQ	1/1:27:4.03	0/1:26:3.0	0/0:16:2.0
-1	10006296	.	C	T	42.23	PASS	AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0	GT:DP:GQ	0/1:7:2000000	./.	./.
-1	10023478	.	G	C,A,T	84.23	.	AF=1.00,0.00,0.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0	GT:DP:GQ	1/1:27:4.03	2/2:26:3.0	0/3:16:2.0
-1	10029362	.	T	C	52.22	.	AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0	GT:DP:GQ	./.	1/0:-1:36.62	./.
-1	10042312	.	G	C	31.81	.	AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0	GT:DP:GQ	1/0:.:5.85	0/0	0/1:4
-1	10044557	.	C	T	62.22	.	AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0	GT:DP:GQ	./.	./.	0/1:31:15.01
-1	10045603	.	AAAA	A	40.26	PASS	AF=0.50	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
-1	10045604	.	A	ACAT	41.26	PASS	AF=0.50	GT:DP:GQ	1/1:14:6.94	0/0:15:7.94	1/0:15:7.94
-1	10048142	.	A	G	126.81	foo	AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
-1	10048580	.	T	A	72.22	bar;baz	AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94

public/testdata/complexExample1.vcf

@@ -1,30 +0,0 @@
-##fileformat=VCFv4.0
-##source=ArbitrarySource
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=HomopolymerRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
-##INFO=<ID=MAPQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=AlleleBalance,Number=1,Type=Float,Description="Allele balance (old name)">
-##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples">
-##INFO=<ID=OnOffGenotype,Number=1,Type=Float,Description="???">
-##INFO=<ID=SpanningDeletions,Number=1,Type=Integer,Description="Number of spanning deletions">
-##INFO=<ID=RMSMAPQ,Number=1,Type=Float,Description="RMS mapping quality (old name)">
-##INFO=<ID=FisherStrand,Number=1,Type=Float,Description="Fisher strand (old name)">
-##INFO=<ID=DoC,Number=1,Type=Integer,Description="DP (old name)">
-##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
-##reference=human_b36_both.fasta
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-1	10001292	testid1	G	A	12.22	PASS	AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0	GT:DP:GQ	1/0:23:19.27	./.	./.
-1	10002963	.	C	G	22.22	.	AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0	GT:DP:GQ	0/1:30:33.07	./.	./.
-1	10005008	.	A	T,C	123.78	PASS	AF=1.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1	GT:DP:GQ	1/1:27:4.03	0/1:26:3.0	0/0:16:2.0
-1	10006296	.	C	T	42.23	PASS	AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0	GT:DP:GQ	0/1:7:2000000	./.	./.
-1	10023478	.	G	C,A,T	84.23	.	AF=1.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0	GT:DP:GQ	1/1:27:4.03	2/2:26:3.0	0/3:16:2.0
-1	10029362	.	T	C	52.22	.	AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0	GT:DP:GQ	./.	1/0:-1:36.62	./.
-1	10042312	.	G	C	31.81	.	AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0	GT:DP:GQ	1/0:.:5.85	0/0	0/1:4
-1	10044557	.	C	T	62.22	.	AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0	GT:DP:GQ	./.	./.	0/1:31:15.01
-1	10045603	.	AAAA	A	40.26	PASS	AF=0.50	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
-1	10045604	.	A	ACAT	41.26	PASS	AF=0.50	GT:DP:GQ	1/1:14:6.94	0/0:15:7.94	1/0:15:7.94
-1	10048142	.	A	G	126.81	foo	AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
-1	10048580	.	T	A	72.22	bar;baz	AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94

public/testdata/complexExample2.vcf

@@ -1,23 +0,0 @@
-##fileformat=VCFv4.0
-##source=ArbitrarySource
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
-##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
-##reference=human_b36_both.fasta
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-1	10001292	testid1	G	A	12.22	PASS	AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0	GT:DP:GQ	1/0:23:19.27	./.	./.
-1	10002963	.	C	G	22.22	.	AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0	GT:DP:GQ	0/1:30:33.07	./.	./.
-1	10005008	.	A	T,C	123.78	PASS	AF=1.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1	GT:DP:GQ	1/1:27:4.03	0/1:26:3.0	0/0:16:2.0
-1	10006296	.	C	T	42.23	PASS	AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0	GT:DP:GQ	0/1:7:2000000	./.	./.
-1	10023478	.	G	C,A,T	84.23	.	AF=1.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0	GT:DP:GQ	1/1:27:4.03	2/2:26:3.0	0/3:16:2.0
-1	10029362	.	T	C	52.22	.	AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0	GT:DP:GQ	./.	1/0:-1:36.62	./.
-1	10042312	.	G	C	31.81	.	AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0	GT:DP:GQ	1/0:.:5.85	0/0	0/1:4
-1	10044557	.	C	T	62.22	.	AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0	GT:DP:GQ	./.	./.	0/1:31:15.01
-1	10045603	.	AAAA	A	40.26	PASS	AF=0.50	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
-1	10045604	.	A	ACAT	41.26	PASS	AF=0.50	GT:DP:GQ	1/1:14:6.94	0/0:15:7.94	1/0:15:7.94
-1	10048142	.	A	G	126.81	foo	AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
-1	10048580	.	T	A	72.22	bar;baz	AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94

public/testdata/complexExample3.vcf

@@ -1,23 +0,0 @@
-##fileformat=VCFv4.0
-##source=ArbitrarySource
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
-##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
-##reference=human_b36_both.fasta
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-1	10001292	testid1	G	A	12.22	PASS	AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0	GT:DP:GQ	1/0:23:19.27	./.	./.
-1	10002963	.	C	G	22.22	.	AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0	GT:DP:GQ	0/1:30:33.07	./.	./.
-1	10005008	.	A	T,C	123.78	PASS	AF=1.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1	GT:DP:GQ	1/1:27:4.03	0/1:26:3.0	0/0:16:2.0
-1	10006296	.	C	T	42.23	PASS	AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0	GT:DP:GQ	0/1:7:2000000	./.	./.
-1	10023478	.	G	C,A,T	84.23	.	AF=1.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0	GT:DP:GQ	1/1:27:4.03	2/2:26:3.0	0/3:16:2.0
-1	10029362	.	T	C	52.22	.	AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0	GT:DP:GQ	./.	1/0:-1:36.62	./.
-1	10042312	.	G	C	31.81	.	AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0	GT:DP:GQ	1/0:.:5.85	0/0	0/1:4
-1	10044557	.	C	T	62.22	.	AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0	GT:DP:GQ	./.	./.	0/1:31:15.01
-1	10045603	.	AAAA	A	40.26	PASS	AF=0.50	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
-1	10045604	.	A	ACAT	41.26	PASS	AF=0.50	GT:DP:GQ	1/1:14:6.94	0/0:15:7.94	1/0:15:7.94
-1	10048142	.	A	G	126.81	foo	AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
-1	10048580	.	T	A	72.22	bar;baz	AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94

public/testdata/dbsnp_135.b37.1000.vcf

@@ -1,249 +0,0 @@
-##fileformat=VCFv4.1
-##FILTER=<ID=NC,Description="Inconsistent Genotype Submission For At Least One Sample">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=ASP,Number=0,Type=Flag,Description="Is Assembly specific. This is set if the variant only maps to one assembly">
-##INFO=<ID=ASS,Number=0,Type=Flag,Description="In acceptor splice site FxnCode = 73">
-##INFO=<ID=CDA,Number=0,Type=Flag,Description="Variation is interrogated in a clinical diagnostic assay">
-##INFO=<ID=CFL,Number=0,Type=Flag,Description="Has Assembly conflict. This is for weight 1 and 2 variant that maps to different chromosomes on different assemblies.">
-##INFO=<ID=CLN,Number=0,Type=Flag,Description="Variant is Clinical(LSDB,OMIM,TPA,Diagnostic)">
-##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75">
-##INFO=<ID=G5,Number=0,Type=Flag,Description=">5% minor allele frequency in 1+ populations">
-##INFO=<ID=G5A,Number=0,Type=Flag,Description=">5% minor allele frequency in each and all populations">
-##INFO=<ID=GCF,Number=0,Type=Flag,Description="Has Genotype Conflict Same (rs, ind), different genotype.  N/N is not included.">
-##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id.  The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">
-##INFO=<ID=GMAF,Number=1,Type=Float,Description="Global Minor Allele Frequency [0, 0.5]; global population is 1000GenomesProject phase 1 genotype data from 629 individuals, released in the 08-04-2010 dataset">
-##INFO=<ID=GNO,Number=0,Type=Flag,Description="Genotypes available. The variant has individual genotype (in SubInd table).">
-##INFO=<ID=HD,Number=0,Type=Flag,Description="Marker is on high density genotyping kit (50K density or greater).  The variant may have phenotype associations present in dbGaP.">
-##INFO=<ID=INT,Number=0,Type=Flag,Description="In Intron FxnCode = 6">
-##INFO=<ID=KGPROD,Number=0,Type=Flag,Description="1000 Genome production phase">
-##INFO=<ID=KGPilot1,Number=0,Type=Flag,Description="1000 Genome discovery(pilot1) 2009">
-##INFO=<ID=KGPilot123,Number=0,Type=Flag,Description="1000 Genome discovery all pilots 2010(1,2,3)">
-##INFO=<ID=KGVAL,Number=0,Type=Flag,Description="1000 Genome validated by second method">
-##INFO=<ID=LSD,Number=0,Type=Flag,Description="Submitted from a locus-specific database">
-##INFO=<ID=MTP,Number=0,Type=Flag,Description="Microattribution/third-party annotation(TPA:GWAS,PAGE)">
-##INFO=<ID=MUT,Number=0,Type=Flag,Description="Is mutation (journal citation, explicit fact): a low frequency variation that is cited in journal and other reputable sources">
-##INFO=<ID=NOC,Number=0,Type=Flag,Description="Contig allele not present in variant allele list. The reference sequence allele at the mapped position is not present in the variant allele list, adjusted for orientation.">
-##INFO=<ID=NOV,Number=0,Type=Flag,Description="Rs cluster has non-overlapping allele sets. True when rs set has more than 2 alleles from different submissions and these sets share no alleles in common.">
-##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
-##INFO=<ID=NSF,Number=0,Type=Flag,Description="Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44">
-##INFO=<ID=NSM,Number=0,Type=Flag,Description="Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42">
-##INFO=<ID=NSN,Number=0,Type=Flag,Description="Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41">
-##INFO=<ID=OM,Number=0,Type=Flag,Description="Has OMIM/OMIA">
-##INFO=<ID=OTH,Number=0,Type=Flag,Description="Has other variant with exactly the same set of mapped positions on NCBI refernce assembly.">
-##INFO=<ID=PH1,Number=0,Type=Flag,Description="Phase 1 genotyped: filtered, non-redundant">
-##INFO=<ID=PH2,Number=0,Type=Flag,Description="Phase 2 genotyped: filtered, non-redundant">
-##INFO=<ID=PH3,Number=0,Type=Flag,Description="Phase 3 genotyped: filtered, non-redundant">
-##INFO=<ID=PM,Number=0,Type=Flag,Description="Variant is Precious(Clinical,Pubmed Cited)">
-##INFO=<ID=PMC,Number=0,Type=Flag,Description="Links exist to PubMed Central article">
-##INFO=<ID=R3,Number=0,Type=Flag,Description="In 3' gene region FxnCode = 13">
-##INFO=<ID=R5,Number=0,Type=Flag,Description="In 5' gene region FxnCode = 15">
-##INFO=<ID=REF,Number=0,Type=Flag,Description="Has reference A coding region variation where one allele in the set is identical to the reference sequence. FxnCode = 8">
-##INFO=<ID=RSPOS,Number=1,Type=Integer,Description="Chr position reported in dbSNP">
-##INFO=<ID=RV,Number=0,Type=Flag,Description="RS orientation is reversed">
-##INFO=<ID=S3D,Number=0,Type=Flag,Description="Has 3D structure - SNP3D table">
-##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
-##INFO=<ID=SCS,Number=1,Type=Integer,Description="Variant Clinical Significance, 0 - unknown, 1 - untested, 2 - non-pathogenic, 3 - probable-non-pathogenic, 4 - probable-pathogenic, 5 - pathogenic, 6 - drug-response, 7 - histocompatibility, 255 - other">
-##INFO=<ID=SLO,Number=0,Type=Flag,Description="Has SubmitterLinkOut - From SNP->SubSNP->Batch.link_out">
-##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Code, 0 - unspecified, 1 - Paralog, 2 - byEST, 3 - Para_EST, 4 - oldAlign, 5 - other">
-##INFO=<ID=SYN,Number=0,Type=Flag,Description="Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3">
-##INFO=<ID=TPA,Number=0,Type=Flag,Description="Provisional Third Party Annotation(TPA) (currently rs from PHARMGKB who will give phenotype data)">
-##INFO=<ID=U3,Number=0,Type=Flag,Description="In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53">
-##INFO=<ID=U5,Number=0,Type=Flag,Description="In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55">
-##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class">
-##INFO=<ID=VLD,Number=0,Type=Flag,Description="Is Validated.  This bit is set if the variant has 2+ minor allele count based on frequency or genotype data.">
-##INFO=<ID=VP,Number=1,Type=String,Description="Variation Property">
-##INFO=<ID=WGT,Number=1,Type=Integer,Description="Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more">
-##INFO=<ID=WTD,Number=0,Type=Flag,Description="Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set.  If all member ss' are withdrawn, then the rs is deleted to SNPHistory">
-##INFO=<ID=dbSNPBuildID,Number=1,Type=Integer,Description="First dbSNP Build for RS">
-##LeftAlignVariants="analysis_type=LeftAlignVariants input_file=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=00-All.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub filter_mismatching_base_and_quals=false"
-##contig=<ID=1,length=249250621,assembly=b37>
-##contig=<ID=10,length=135534747,assembly=b37>
-##contig=<ID=11,length=135006516,assembly=b37>
-##contig=<ID=12,length=133851895,assembly=b37>
-##contig=<ID=13,length=115169878,assembly=b37>
-##contig=<ID=14,length=107349540,assembly=b37>
-##contig=<ID=15,length=102531392,assembly=b37>
-##contig=<ID=16,length=90354753,assembly=b37>
-##contig=<ID=17,length=81195210,assembly=b37>
-##contig=<ID=18,length=78077248,assembly=b37>
-##contig=<ID=19,length=59128983,assembly=b37>
-##contig=<ID=2,length=243199373,assembly=b37>
-##contig=<ID=20,length=63025520,assembly=b37>
-##contig=<ID=21,length=48129895,assembly=b37>
-##contig=<ID=22,length=51304566,assembly=b37>
-##contig=<ID=3,length=198022430,assembly=b37>
-##contig=<ID=4,length=191154276,assembly=b37>
-##contig=<ID=5,length=180915260,assembly=b37>
-##contig=<ID=6,length=171115067,assembly=b37>
-##contig=<ID=7,length=159138663,assembly=b37>
-##contig=<ID=8,length=146364022,assembly=b37>
-##contig=<ID=9,length=141213431,assembly=b37>
-##contig=<ID=GL000191.1,length=106433,assembly=b37>
-##contig=<ID=GL000192.1,length=547496,assembly=b37>
-##contig=<ID=GL000193.1,length=189789,assembly=b37>
-##contig=<ID=GL000194.1,length=191469,assembly=b37>
-##contig=<ID=GL000195.1,length=182896,assembly=b37>
-##contig=<ID=GL000196.1,length=38914,assembly=b37>
-##contig=<ID=GL000197.1,length=37175,assembly=b37>
-##contig=<ID=GL000198.1,length=90085,assembly=b37>
-##contig=<ID=GL000199.1,length=169874,assembly=b37>
-##contig=<ID=GL000200.1,length=187035,assembly=b37>
-##contig=<ID=GL000201.1,length=36148,assembly=b37>
-##contig=<ID=GL000202.1,length=40103,assembly=b37>
-##contig=<ID=GL000203.1,length=37498,assembly=b37>
-##contig=<ID=GL000204.1,length=81310,assembly=b37>
-##contig=<ID=GL000205.1,length=174588,assembly=b37>
-##contig=<ID=GL000206.1,length=41001,assembly=b37>
-##contig=<ID=GL000207.1,length=4262,assembly=b37>
-##contig=<ID=GL000208.1,length=92689,assembly=b37>
-##contig=<ID=GL000209.1,length=159169,assembly=b37>
-##contig=<ID=GL000210.1,length=27682,assembly=b37>
-##contig=<ID=GL000211.1,length=166566,assembly=b37>
-##contig=<ID=GL000212.1,length=186858,assembly=b37>
-##contig=<ID=GL000213.1,length=164239,assembly=b37>
-##contig=<ID=GL000214.1,length=137718,assembly=b37>
-##contig=<ID=GL000215.1,length=172545,assembly=b37>
-##contig=<ID=GL000216.1,length=172294,assembly=b37>
-##contig=<ID=GL000217.1,length=172149,assembly=b37>
-##contig=<ID=GL000218.1,length=161147,assembly=b37>
-##contig=<ID=GL000219.1,length=179198,assembly=b37>
-##contig=<ID=GL000220.1,length=161802,assembly=b37>
-##contig=<ID=GL000221.1,length=155397,assembly=b37>
-##contig=<ID=GL000222.1,length=186861,assembly=b37>
-##contig=<ID=GL000223.1,length=180455,assembly=b37>
-##contig=<ID=GL000224.1,length=179693,assembly=b37>
-##contig=<ID=GL000225.1,length=211173,assembly=b37>
-##contig=<ID=GL000226.1,length=15008,assembly=b37>
-##contig=<ID=GL000227.1,length=128374,assembly=b37>
-##contig=<ID=GL000228.1,length=129120,assembly=b37>
-##contig=<ID=GL000229.1,length=19913,assembly=b37>
-##contig=<ID=GL000230.1,length=43691,assembly=b37>
-##contig=<ID=GL000231.1,length=27386,assembly=b37>
-##contig=<ID=GL000232.1,length=40652,assembly=b37>
-##contig=<ID=GL000233.1,length=45941,assembly=b37>
-##contig=<ID=GL000234.1,length=40531,assembly=b37>
-##contig=<ID=GL000235.1,length=34474,assembly=b37>
-##contig=<ID=GL000236.1,length=41934,assembly=b37>
-##contig=<ID=GL000237.1,length=45867,assembly=b37>
-##contig=<ID=GL000238.1,length=39939,assembly=b37>
-##contig=<ID=GL000239.1,length=33824,assembly=b37>
-##contig=<ID=GL000240.1,length=41933,assembly=b37>
-##contig=<ID=GL000241.1,length=42152,assembly=b37>
-##contig=<ID=GL000242.1,length=43523,assembly=b37>
-##contig=<ID=GL000243.1,length=43341,assembly=b37>
-##contig=<ID=GL000244.1,length=39929,assembly=b37>
-##contig=<ID=GL000245.1,length=36651,assembly=b37>
-##contig=<ID=GL000246.1,length=38154,assembly=b37>
-##contig=<ID=GL000247.1,length=36422,assembly=b37>
-##contig=<ID=GL000248.1,length=39786,assembly=b37>
-##contig=<ID=GL000249.1,length=38502,assembly=b37>
-##contig=<ID=MT,length=16569,assembly=b37>
-##contig=<ID=X,length=155270560,assembly=b37>
-##contig=<ID=Y,length=59373566,assembly=b37>
-##dbSNP_BUILD_ID=135
-##fileDate=20111104
-##phasing=partial
-##reference=GRCh37.3
-##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
-##source=dbSNP
-##variationPropertyDocumentationUrl=ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf	
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	
-1	10144	rs144773400	TA	T	.	PASS	ASP;RSPOS=10145;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
-1	10228	rs143255646	TA	T	.	PASS	ASP;RSPOS=10229;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
-1	10234	rs145599635	C	T	.	PASS	ASP;RSPOS=10234;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	10248	rs148908337	A	T	.	PASS	ASP;RSPOS=10248;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	10254	rs140194106	TA	T	.	PASS	ASP;RSPOS=10255;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
-1	10291	rs145427775	C	T	.	PASS	ASP;RSPOS=10291;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	10327	rs112750067	T	C	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=10327;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
-1	10329	rs150969722	AC	A	.	PASS	ASP;RSPOS=10330;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
-1	10351	rs145072688	CTA	C,CA	.	PASS	ASP;RSPOS=10352;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
-1	10382	rs147093981	AAC	A,AC	.	PASS	ASP;RSPOS=10383;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
-1	10433	rs56289060	A	AC	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=10433;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
-1	10439	rs112766696	AC	A	.	PASS	ASP;GENEINFO=LOC100652771:100652771;GNO;RSPOS=10440;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000004000100000200;WGT=0;dbSNPBuildID=132
-1	10439	rs138941843	AC	A	.	PASS	ASP;RSPOS=10440;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=134
-1	10440	rs112155239	C	A	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=10440;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=132
-1	10492	rs55998931	C	T	.	PASS	ASP;GENEINFO=LOC100652771:100652771;GMAF=0.0617001828153565;RSPOS=10492;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040000000100;WGT=0;dbSNPBuildID=129
-1	10519	rs62636508	G	C	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=10519;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
-1	10583	rs58108140	G	A	.	PASS	ASP;GENEINFO=LOC100652771:100652771;GMAF=0.270566727605119;KGPilot123;RSPOS=10583;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040010000100;WGT=0;dbSNPBuildID=129
-1	10611	rs189107123	C	G	.	PASS	KGPilot123;RSPOS=10611;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	10828	rs10218492	G	A	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=10828;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=119
-1	10904	rs10218493	G	A	.	PASS	ASP;GENEINFO=LOC100652771:100652771;GNO;RSPOS=10904;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=119
-1	10927	rs10218527	A	G	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=10927;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=119
-1	10938	rs28853987	G	A	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=10938;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=125
-1	11014	rs28484712	G	A	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=11014;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=125
-1	11022	rs28775022	G	A	.	PASS	ASP;GENEINFO=LOC100652771:100652771;RSPOS=11022;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=125
-1	11081	rs10218495	G	T	.	PASS	CFL;GENEINFO=LOC100652771:100652771;GNO;RSPOS=11081;SAO=0;SSR=0;VC=SNV;VP=050000000008000100000100;WGT=0;dbSNPBuildID=119
-1	11863	rs187669455	C	A	.	PASS	RSPOS=11863;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
-1	13302	rs180734498	C	T	.	PASS	KGPilot123;RSPOS=13302;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	13327	rs144762171	G	C	.	PASS	ASP;KGPilot123;RSPOS=13327;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	13684	rs71260404	C	T	.	PASS	GENEINFO=LOC100652771:100652771;GNO;RSPOS=13684;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000100000100;WGT=0;dbSNPBuildID=130
-1	13980	rs151276478	T	C	.	PASS	ASP;KGPilot123;RSPOS=13980;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	14889	rs142444908	G	A	.	PASS	ASP;RSPOS=14889;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	14907	rs79585140	A	G	.	PASS	GNO;RSPOS=14907;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=131
-1	14930	rs75454623	A	G	.	PASS	GNO;RSPOS=14930;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=131
-1	14976	rs71252251	G	A	.	PASS	ASP;GNO;RSPOS=14976;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=130
-1	15061	rs71268703	T	TG	.	PASS	ASP;GNO;RSPOS=15061;RV;SAO=0;SLO;SSR=0;VC=DIV;VP=050100000004000100000200;WGT=0;dbSNPBuildID=130
-1	15118	rs71252250	A	G	.	PASS	ASP;GNO;RSPOS=15118;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000004000100000100;WGT=0;dbSNPBuildID=130
-1	15211	rs144718396	T	G	.	PASS	ASP;RSPOS=15211;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	15211	rs78601809	T	G	.	PASS	ASP;GNO;RSPOS=15211;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
-1	16257	rs78588380	G	C	.	PASS	ASP;GNO;RSPOS=16257;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
-1	16378	rs148220436	T	C	.	PASS	ASP;RSPOS=16378;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	16495	rs141130360	G	C	.	PASS	ASP;RSPOS=16495;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	16497	rs150723783	A	G	.	PASS	ASP;RSPOS=16497;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	17519	rs192890528	G	T	.	PASS	RSPOS=17519;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=135
-1	19226	rs138930629	T	A	.	PASS	ASP;RSPOS=19226;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	20141	rs56336884	G	A	.	PASS	HD;RSPOS=20141;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000400000100;WGT=0;dbSNPBuildID=129
-1	20144	rs143346096	G	A	.	PASS	ASP;RSPOS=20144;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	20206	rs71262675	C	T	.	PASS	GNO;RSPOS=20206;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000100000100;WGT=0;dbSNPBuildID=130
-1	20245	rs71262674	G	A	.	PASS	GMAF=0.256398537477148;GNO;RSPOS=20245;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000100000100;WGT=0;dbSNPBuildID=130
-1	20304	rs71262673	G	C	.	PASS	GMAF=0.338208409506399;GNO;RSPOS=20304;RV;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000000100000100;WGT=0;dbSNPBuildID=130
-1	26999	rs147506580	A	G	.	PASS	ASP;RSPOS=26999;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	29436	rs2462493	G	A	.	PASS	GNO;RSPOS=29436;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=100
-1	30923	rs140337953	G	T	.	PASS	ASP;KGPilot123;RSPOS=30923;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	33487	rs77459554	C	T	.	PASS	ASP;GNO;RSPOS=33487;SAO=0;SSR=0;VC=SNV;VP=050000000004000100000100;WGT=0;dbSNPBuildID=131
-1	33495	rs75468675	C	T	.	PASS	ASP;GNO;RSPOS=33495;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
-1	33505	rs75627161	T	C	.	PASS	ASP;GNO;RSPOS=33505;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
-1	33508	rs75609629	A	T	.	PASS	ASP;GNO;RSPOS=33508;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040100000100;WGT=0;dbSNPBuildID=131
-1	33521	rs76098219	T	A	.	PASS	GNO;RSPOS=33521;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040100000100;WGT=0;dbSNPBuildID=131
-1	33593	rs557585	G	A	.	PASS	RSPOS=33593;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=83
-1	33648	rs62028204	G	T	.	PASS	RSPOS=33648;RV;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=129
-1	33656	rs113821789	T	C	.	PASS	RSPOS=33656;RV;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=132
-1	51476	rs187298206	T	C	.	PASS	KGPilot123;RSPOS=51476;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	51479	rs116400033	T	A	.	PASS	ASP;G5;G5A;GMAF=0.113802559414991;KGPilot123;RSPOS=51479;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004070010000100;WGT=0;dbSNPBuildID=132
-1	51803	rs62637812	T	C	.	PASS	GMAF=0.468921389396709;RSPOS=51803;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000000040000000100;WGT=0;dbSNPBuildID=129
-1	51898	rs76402894	C	A	.	PASS	GMAF=0.0731261425959781;GNO;RSPOS=51898;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
-1	51914	rs190452223	T	G	.	PASS	KGPilot123;RSPOS=51914;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	51928	rs78732933	G	A	.	PASS	GNO;RSPOS=51928;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=131
-1	51935	rs181754315	C	T	.	PASS	KGPilot123;RSPOS=51935;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	51954	rs185832753	G	C	.	PASS	KGPilot123;RSPOS=51954;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	52058	rs62637813	G	C	.	PASS	GMAF=0.0342778793418647;KGPilot123;RSPOS=52058;SAO=0;SSR=1;VC=SNV;VLD;VP=050000000000040010000140;WGT=0;dbSNPBuildID=129
-1	52144	rs190291950	T	A	.	PASS	KGPilot123;RSPOS=52144;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	52238	rs150021059	T	G	.	PASS	ASP;KGPilot123;RSPOS=52238;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	54353	rs140052487	C	A	.	PASS	ASP;KGPilot123;RSPOS=54353;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	54421	rs146477069	A	G	.	PASS	ASP;KGPilot123;RSPOS=54421;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	54490	rs141149254	G	A	.	PASS	ASP;KGPilot123;RSPOS=54490;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	54676	rs2462492	C	T	.	PASS	ASP;GMAF=0.191956124314442;GNO;HD;KGPilot123;RSPOS=54676;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004040510000100;WGT=0;dbSNPBuildID=100
-1	54753	rs143174675	T	G	.	PASS	ASP;KGPilot123;RSPOS=54753;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	54788	rs59861892	CC	C,CCT	.	PASS	ASP;RSPOS=54789;SAO=0;SSR=0;VC=DIV;VP=050000000004000000000200;WGT=0;dbSNPBuildID=129
-1	54795	rs58014817	T	A	.	PASS	ASP;RSPOS=54795;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=129
-1	55164	rs3091274	C	A	.	PASS	G5;G5A;GMAF=0.145338208409506;GNO;KGPilot123;RSPOS=55164;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000030110000100;WGT=0;dbSNPBuildID=103
-1	55299	rs10399749	C	T	.	PASS	G5;G5A;GMAF=0.278793418647166;GNO;KGPilot123;PH2;RSPOS=55299;SAO=0;SLO;SSR=0;VC=SNV;VP=050100000000030112000100;WGT=0;dbSNPBuildID=119
-1	55302	rs3091273	C	T	.	PASS	RSPOS=55302;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=103
-1	55313	rs182462964	A	T	.	PASS	KGPilot123;RSPOS=55313;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	55322	rs3107974	C	T	.	PASS	RSPOS=55322;SAO=0;SSR=0;VC=SNV;VP=050000000000000000000100;WGT=0;dbSNPBuildID=103
-1	55326	rs3107975	T	C	.	PASS	GNO;HD;KGPilot123;RSPOS=55326;SAO=0;SSR=0;VC=SNV;VP=050000000000000510000100;WGT=0;dbSNPBuildID=103
-1	55330	rs185215913	G	A	.	PASS	KGPilot123;RSPOS=55330;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	55367	rs190850374	G	A	.	PASS	KGPilot123;RSPOS=55367;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	55388	rs182711216	C	T	.	PASS	KGPilot123;RSPOS=55388;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	55394	rs2949420	T	A	.	PASS	GNO;KGPilot123;PH2;RSPOS=55394;SAO=0;SSR=0;VC=SNV;VP=050000000000000112000100;WGT=0;dbSNPBuildID=101
-1	55416	rs193242050	G	A	.	PASS	KGPilot123;RSPOS=55416;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	55427	rs183189405	T	C	.	PASS	KGPilot123;RSPOS=55427;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	55545	rs28396308	C	T	.	PASS	GNO;RSPOS=55545;SAO=0;SSR=0;VC=SNV;VP=050000000000000100000100;WGT=0;dbSNPBuildID=125
-1	55816	rs187434873	G	A	.	PASS	KGPilot123;RSPOS=55816;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	55850	rs191890754	C	G	.	PASS	KGPilot123;RSPOS=55850;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	55852	rs184233019	G	C	.	PASS	KGPilot123;RSPOS=55852;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	56644	rs143342222	A	C	.	PASS	ASP;KGPilot123;RSPOS=56644;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134
-1	57952	rs189727433	A	C	.	PASS	KGPilot123;RSPOS=57952;SAO=0;SSR=0;VC=SNV;VP=050000000000000010000100;WGT=0;dbSNPBuildID=135
-1	58771	rs140128481	T	C	.	PASS	ASP;RSPOS=58771;SAO=0;SSR=0;VC=SNV;VP=050000000004000000000100;WGT=0;dbSNPBuildID=134
-1	58814	rs114420996	G	A	.	PASS	ASP;G5;GMAF=0.0982632541133455;KGPilot123;RSPOS=58814;SAO=0;SSR=0;VC=SNV;VLD;VP=050000000004050010000100;WGT=0;dbSNPBuildID=132
-1	59040	rs149755937	T	C	.	PASS	ASP;KGPilot123;RSPOS=59040;SAO=0;SSR=0;VC=SNV;VP=050000000004000010000100;WGT=0;dbSNPBuildID=134

public/testdata/defaultGATKConfig.cfg

@@ -1,26 +0,0 @@
-[DEFAULT]
-jar: ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar
-referenceRoot: /home/radon01/depristo/work/humanref/Homo_sapiens_assembly18
-reference: %(referenceRoot)s.fasta
-referenceIndex: %(reference)s.fai
-referenceDict: %(referenceRoot)s.dict
-java: java
-jvm_args: -ea -Xmx2048m
-gatkData: /humgen/gsa-scr1/GATK_Data
-dbsnp: %(gatkData)s/dbsnp_129_hg18.rod
-tmp: /tmp/
-args: -l INFO
-Sting: ~/dev/GenomeAnalysisTK/trunk
-#args: -l INFO -L chr1:1-1,000,000
-
-[CountCovariates]
-args: --MIN_MAPPING_QUALITY 1 -D %(dbsnp)s
-
-[TableRecalibration]
-args: -compress 1
-
-[R]
-Rscript: /broad/tools/apps/R-2.6.0/bin/Rscript 
-PlotQEmpStated: %(Sting)s/R/plot_q_emp_stated_hst.R
-PlotQDiffByCycle: %(Sting)s/R/plot_qual_diff_v_cycle.R
-PlotQDiffByDinuc: %(Sting)s/R/plot_qual_diff_v_dinuc.R

public/testdata/diffTestMaster.vcf

@@ -1,11 +0,0 @@
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
-chr1	2646	rs62635284	G	A	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:53,75:3:-12.40,-0.90,-0.00:9.03
-chr1	2979	rs62635286	T	G	83.67	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,32:9:-33.61,-2.71,-0.00:27.09
-chr1	2981	rs62028691	A	G	14.69	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,33:9:-32.12,-2.71,-0.00:27.08
-chr1	4536	rs11582131	G	C	0.18	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:42,33:16:-41.67,-4.82,-26.29:99
-chr1	4562	rs11490464	C	G	0.14	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:26,30:9:-19.64,-2.72,-14.87:99
-chr1	4770	rs6682375	A	G	0.32	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:9,111:84:-306.27,-28.58,-3.46:99
-chr1	4793	rs6682385	A	G	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:4,115:109:-350.74,-32.88,-0.10:99
-chr1	5074	rs11586607	T	G	0.01	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:29,97:39:-130.41,-11.75,-3.82:79.31
-chr1	5137	rs62636497	A	T	140.49	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:0,74:39:-148.99,-11.75,-0.01:99

public/testdata/diffTestTest.vcf

@@ -1,11 +0,0 @@
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
-chr1	2646	rs62635284	G	A	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:53,75:3:-12.40,-0.90,-0.00:9.03
-chr1	2979	rs62635286	T	G	83.67	CHANGED_FILTER	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,32:9:-33.61,-2.71,-0.00:27.09
-chr1	2981	rs62028691	A	G	14.69	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:31,33:9:-32.12,-2.71,-0.00:27.08
-chr1	4536	rs11582131	G	C	0.18	PASS	AC=2;AF=0.50;AN=2	GT:AD:DP:GL:GQ	0/1:42,33:16:-41.67,-4.82,-26.29:99
-chr1	4562	rs11490464	C	G	0.14	PASS	AC=1;AF=0.50;AN=2	GT:AD:DP:GL:GQ	1/1:26,30:9:-19.64,-2.72,-14.87:99
-chr1	4770	rs6682375	A	G	0.32	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	0/1:9,111:84:-306.27,-28.58,-3.46:99
-chr1	4793	rs6682385	A	G	0.15	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:4,114:109:-350.74,-32.88,-0.10:99
-chr1	5074	rs11586607	T	G	0.01	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:29,97:39:-130.41,-11.74,-3.82:79.31
-chr1	5137	rs62636497	A	T	140.49	PASS	AC=2;AF=1.00;AN=2	GT:AD:DP:GL:GQ	1/1:0,74:39:-148.99,-11.75,-0.01:9

public/testdata/fakeHM3.vcf

@@ -1,9 +0,0 @@
-##fileformat=VCFv4.0
-##INFO=<ID=XX,Number=0,Type=Flag,Description="XX Membership">
-##FOO
-##BAR
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	
-1	10001292	.	G	A	.	PASS	.	GT	1/0
-1	10006296	.	C	T	.	PASS	.	GT	0/1
-1	10042312	.	G	C	.	FAIL	.	GT	1/0
-1	10048142	.	A	G	.	PASS	.	GT	1/1

public/testdata/forLeftAlignVariantsTest.vcf

@@ -1,5 +0,0 @@
-##fileformat=VCFv4.0
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-1	194723643	rs67631353	CA	CCC	.	.	.
-2	179391647	.	T	TT	.	.	.
-20	120123	rs34533099	A	AGA	.	.	.

public/testdata/gFFTest.gff

@@ -1,7 +0,0 @@
-SEQ1	EMBL	atg	103	105	.	+	0
-SEQ1	EMBL	exon	103	172	.	+	0
-SEQ1	EMBL	splice5	172	173	.	+	.
-SEQ1	netgene	splice5	172	173	0.94	+	.
-SEQ1	genie	sp5-20	163	182	2.3	+	.
-SEQ1	genie	sp5-10	168	177	2.1	+	.
-SEQ2	grail	ATG	17	19	2.1	-	0

public/testdata/gatkrunreport.fail.xml

@@ -1,50 +0,0 @@
-<GATK-run-report>
-   <id>yX3AnltsqIlXH9kAQqTWHQUd8CQ5bikz</id>   
-   <exception>
-      <message>Failed to parse Genome Location string:
-      20:10,000,000-10,000,001x</message>
-      <stacktrace class="java.util.ArrayList"> 
-         <string>org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(GenomeLocParser.java:377)</string>
-         <string>org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:82)</string>
-         <string>org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(IntervalBinding.java:106)</string>
-         <string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.loadIntervals(GenomeAnalysisEngine.java:618)</string>
-         <string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:585)</string>
-         <string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:231)</string>
-         <string>org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128)</string>
-         <string>org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)</string>
-         <string>org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)</string>
-         <string>org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)</string>
-      </stacktrace>
-      <cause>
-         <message>Position: &apos;10,000,001x&apos; contains invalid
-         chars.</message>
-         <stacktrace class="java.util.ArrayList">
-            <string>org.broadinstitute.sting.utils.GenomeLocParser.parsePosition(GenomeLocParser.java:411)</string>
-            <string>org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(GenomeLocParser.java:374)</string>
-            <string>org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:82)</string>
-            <string>org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(IntervalBinding.java:106)</string>
-            <string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.loadIntervals(GenomeAnalysisEngine.java:618)</string>
-            <string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:585)</string>
-            <string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:231)</string>
-            <string>org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128)</string>
-            <string>org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)</string>
-            <string>org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)</string>
-            <string>org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)</string>
-         </stacktrace>
-         <is-user-exception>false</is-user-exception>
-      </cause>
-      <is-user-exception>true</is-user-exception>
-   </exception>
-   <start-time>2012/03/10 20.19.52</start-time>
-   <end-time>2012/03/10 20.19.52</end-time>
-   <run-time>0</run-time>
-   <walker-name>CountReads</walker-name>
-   <svn-version>1.4-483-g63ecdb2</svn-version>
-   <total-memory>85000192</total-memory>
-   <max-memory>129957888</max-memory>
-   <user-name>depristo</user-name>
-   <host-name>10.0.1.10</host-name>
-   <java>Apple Inc.-1.6.0_26</java>
-   <machine>Mac OS X-x86_64</machine>
-   <iterations>0</iterations>
-</GATK-run-report>

public/testdata/gatkrunreport.success.xml

@@ -1,15 +0,0 @@
-<GATK-run-report>
-   <id>D7D31ULwTSxlAwnEOSmW6Z4PawXwMxEz</id>
-   <start-time>2012/03/10 20.21.19</start-time>
-   <end-time>2012/03/10 20.21.19</end-time>
-   <run-time>0</run-time>
-   <walker-name>CountReads</walker-name>
-   <svn-version>1.4-483-g63ecdb2</svn-version>
-   <total-memory>85000192</total-memory>
-   <max-memory>129957888</max-memory>
-   <user-name>depristo</user-name>
-   <host-name>10.0.1.10</host-name>
-   <java>Apple Inc.-1.6.0_26</java>
-   <machine>Mac OS X-x86_64</machine>
-   <iterations>105</iterations>
-</GATK-run-report>

public/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap

@@ -1,500 +0,0 @@
-rs# alleles chrom pos strand assembly# center protLSID assayLSID panelLSID QCcode NA19625 NA19700 NA19701 NA19702 NA19703 NA19704 NA19705 NA19708 NA19712 NA19711 NA19818 NA19819 NA19828 NA19835 NA19834 NA19836 NA19902 NA19901 NA19900 NA19904 NA19919 NA19908 NA19909 NA19914 NA19915 NA19916 NA19917 NA19918 NA19921 NA20129 NA19713 NA19982 NA19983 NA19714 NA19985 NA19984 NA20128 NA20126 NA20127 NA20277 NA20276 NA20279 NA20282 NA20281 NA20284 NA20287 NA20288 NA20290 NA20289 NA20291 NA20292 NA20295 NA20294 NA20297 NA20300 NA20298 NA20301 NA20302 NA20317 NA20319 NA20322 NA20333 NA20332 NA20335 NA20334 NA20337 NA20336 NA20340 NA20341 NA20343 NA20342 NA20344 NA20345 NA20346 NA20347 NA20348 NA20349 NA20350 NA20351 NA20357 NA20356 NA20358 NA20359 NA20360 NA20363 NA20364 NA20412
-rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs11510103 A/G chr1 557616 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11510103:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA NN AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs11240767 C/T chr1 718814 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11240767:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CT CC CC CT CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CT CC CC CC CT CC CC CC CC NN CC CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CT CT CC CC CT CT CC
-rs3131972 A/G chr1 742584 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3131972:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG AG AA AA AA AA GG AG AG AG AA AG GG AG GG AG AG AG AA GG GG AG AG AG AA AA AA GG AG AA AG AG AG AA AG AG AG GG AA AG AG AG AA GG AA AA GG AG AG AA AA AA AA AA AG GG GG GG AG AA AA AA AA AG AA AG GG AG AG AG AG AG AG AG AG AG AG AA AG AA AG AA AG AA AA AA
-rs3131969 A/G chr1 744045 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3131969:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG AG AA AA AA AA GG AG GG AG AA AG GG AG GG AG AG AG AA GG GG AG AG AG AA AA AA GG AG AA AG AG AG AA NN AG AG GG AG GG GG AG AA GG AA AA GG AG AG NN AA AG AA AA AG GG GG GG AG AA AA NN AA AG AA AG GG AG AG AG AG AG GG AG AG AG AG AA AG AA AG AA AG AA AA AA
-rs1048488 C/T chr1 750775 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1048488:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT TT CT CC CC CC TT CT TT CT CC CT TT CT TT CT CT TT CC TT TT CT CT CT CC CC CC TT CT CC TT CT CT CC CT CT CT TT CT TT CT CT CC TT CC CC TT CT CT CC CT CT CT CC CT TT TT TT CT CC CC CT CT TT CC CT TT CT CT CT CT CT CT CT CT CT CT CC CT CC CT CC CT CC CC CC
-rs12562034 A/G chr1 758311 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12562034:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG GG GG GG GG NN GG AG GG GG GG AG AG AG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG GG GG GG GG GG AG GG GG AG
-rs12124819 A/G chr1 766409 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12124819:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AG AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs4040617 A/G chr1 769185 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4040617:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG AA AG GG GG GG AA AG AA AG GG AG AA AG AA AG AG AA GG AA AA AG AG AG AG GG AG AA AG GG AA AG NN GG AG AG AG AA AG AA AA AG AG AA GG GG AA AG AG GG AG AG AG GG AG AA AA AA AG AA GG AG AG AA GG AG AA AG AG AG AG AG AA AA AG AG AG GG AG AG AA GG AG AG GG GG
-rs2905036 C/T chr1 782343 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2905036:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT CC TT TT TT TT TT TT TT CT TT TT TT TT TT CT TT TT TT TT TT CT CT TT TT CT TT TT
-rs4245756 C/T chr1 789326 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4245756:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CT CT CT CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs12086311 A/G chr1 798632 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12086311:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs4970383 A/C chr1 828418 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4970383:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC AC CC CC CC AA AC AC CC AC CC CC CC AC AC AC AC AC CC AA CC AC CC CC AC AA CC AC CC CC AC AC CC AA AA AC AC CC AC AA AC AA AC AC AC CC AC CC CC AC AC CC AC AC CC AC AC AA AC CC CC CC AC CC CC CC CC AC CC AC AA AC AC CC CC CC AC CC AC AA AC AC AC AC CC AC AC
-rs4475691 C/T chr1 836671 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4475691:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CT CT CC CC CC TT CT CC CC CT CC CT TT CT CC CC CT CC CC CC CC CT CC CT CT TT CC CC CT CC CT CT CT CT TT CT CT CT CT CT TT CC CT CT CT CT CT CC CC CT TT CT CC TT TT TT CT CC CT TT CT CT CC CC CT CT CT CC CT CC CC CC CT CT CC CT CT CT CC CT CC CT CT CT CT
-rs1806509 A/C chr1 843817 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1806509:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC CC CC CC CC AC AC CC CC AA AC AC CC CC CC CC AC AC AA AC AA AC AC AC AA AA CC AC AA AC AC CC CC AC AC AC CC AC AC AC AC AC CC CC AC AC AC AC CC AC AA CC CC AC CC CC CC CC AC AC CC CC AC AC AA CC CC CC CC AC AC CC CC AC AC AC CC CC AC AC AC CC AA AC AC AA CC
-rs7537756 A/G chr1 844113 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7537756:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA GG AG AG AG AA AG AA AA AG AG GG AA AG AA AG AG AA AA AA AA AA AG AA AA AG AG AA AA AA AG AA AG AA AA GG AG AG AA AA AG AG AG AG AA AA AG AG AA AA AA AA AG AA GG GG GG AG AA AG AA AA AG AA AG GG GG AG AA AG AG AG AA AG AG AG AA AA AG AA AG AA AA AG AA AG
-rs6694982 A/G chr1 847691 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6694982:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AG AA AA AA AA AG AG AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AG AG AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA
-rs13302982 A/G chr1 851671 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13302982:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AA AA AG AA AG AG AG AA AA AA AA AA AG AA AG AA AG AA AG AG AG GG AG AA AA AA GG GG AA AG AG AG AG AG GG AG GG AA AG GG AG AA GG AA AA AG AA AG AG AG AG AG GG GG AG GG GG GG AA AA AA GG GG AG AA AA AA AG AG AG AG AG AA AA AG AG AG GG AA AG AG AA AG AG AG
-rs4040604 G/T chr1 852987 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4040604:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GT GG GG GT GG GT GT GT GG GG GG GG GG GT GG GT GG GT GG GT GT GT TT GT GG GG GG TT TT GG GT GT GT GT GT TT GT TT GG GT TT GT GG TT GG GG GT GG GT GT GT GT GT TT TT GT TT TT TT GG GG GG TT TT GT GG GG GG GT GT GT GT GT GG GG GT GT GT TT GG GT GT GG GT GT GT
-rs2340587 A/G chr1 854801 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2340587:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG AG GG AG GG AG GG GG GG GG GG AG GG AG GG AG GG AG AG AG AG AG GG GG GG AA AG GG AG AG GG GG AG GG GG AG GG AG AG GG GG AG GG GG AG GG AG AG AG AG GG AG AG GG GG AA AA GG GG GG AG AG AG GG GG GG AG GG AG AG AG GG GG AG AG AG AA GG AG AG GG AG AG GG
-rs28576697 C/T chr1 860508 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28576697:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT CC CT CT TT TT CT CT TT CT TT TT TT TT TT TT TT TT TT TT TT CT CC TT TT TT TT TT TT TT CT TT TT TT CT CT CT CT CT TT TT CT CT TT TT TT TT TT TT TT TT CT
-rs1110052 G/T chr1 863421 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1110052:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GT GG GG GT GG GT GG GG GG GG GG GG GG GT GG GT GG GT GG GT GT GT GT TT GG GG GG TT GT GT GT TT GT GG GT GG GG GT GG GT GT GG GG GT GG GG GT GG GT GT GG GG GG GT GG GG GG TT TT GG GG GG GT GT GG GG GT GG GG GG GG GG GG GG GG GG GG GT TT GG GT GT GG GT GT GT
-rs7523549 C/T chr1 869180 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7523549:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CC CT CC CT CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CC CT TT TT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CT CC CC CC CT CT CC CC CC CT CC CC CC CT CC CC CC CC CC CC CC CC CC CC CT CC CC CC CT CC CT CT CT
-rs3748592 A/G chr1 870101 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3748592:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG AG AG AG AA AG AG AG GG GG
-rs3748593 A/C chr1 870253 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3748593:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC AC CC CC AC CC AC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC AC CC CC CC CC CC AC AA AA CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC CC CC AC CC CC CC AC AC CC CC CC AC CC CC CC AC CC CC CC CC CC CC CC CC CC CC AC CC CC CC AC CC AC AC AC
-rs2272756 A/G chr1 871896 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2272756:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG AA GG GG GG GG GG GG GG AG GG GG GG AG AG AG AG AG GG GG AG AG GG GG GG GG GG GG GG GG AG
-rs2340582 A/G chr1 872666 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2340582:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG AG AG AG AA AG AG AG GG GG
-rs4246503 A/G chr1 874678 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4246503:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG AG AG AG AA AG AG AG GG GG
-rs3748594 A/G chr1 876247 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3748594:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG AG GG AG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG AG AA AA GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG AG GG GG GG AG AG GG GG GG AG GG GG GG AG GG GG GG GG GG GG GG GG GG GG AG GG GG GG AG GG AG AG AG
-rs17160698 C/T chr1 877025 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs17160698:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CT TT CT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT TT TT CT TT TT TT CT CC TT CT CT CT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT
-rs3748595 A/C chr1 877423 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3748595:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC CC AC AC CC AC CC CC CC CC AC CC AC CC AC CC AC AC CC AC CC CC CC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC CC CC CC AC CC CC AC AC CC CC AC CC CC CC CC AC CC CC CC CC CC CC CC AC CC CC CC CC CC AC AC CC CC AC AC AC AA AC AC AC AC CC
-rs13303106 A/G chr1 881808 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13303106:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AG AG AA AA AA AA AA AA AA AA AA AG AG AG AA GG AG AG AG AG AA AG AA GG AG AG AA AA GG AG NN AG GG AG AG AG AG AA AA AG AG AA AG AA AA AA AA AA AA AA AA AA AA AG AG AA AA AG AA AG AA AA AA AA AA AA AA AA AG AG AA AA AA AA AG AG AA AA AA AA AA AA
-rs28415373 C/T chr1 883844 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28415373:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
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-rs28695703 C/T chr1 894218 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28695703:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CC CT CT CC CC CC CT TT CT CC CC CT CT CT CC CC CC CT CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CT CC CC CC CT CT CC CT CT CC CC CC CC CT CC CC CT TT CT CT CC CC CC CC CC CT CT CT CT CT CC CC CT CT CC CC CT CT CC CC CC CT CT CC CC CC CC CC CT CC CC CT
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-rs34831709 A/G chr1 897696 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs34831709:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs28504611 C/T chr1 898277 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28504611:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CC TT CT CC CT CC CC CT CT TT CC CT TT CT TT CT CT CC CT CC CT CC CC CC CT CT CT CC CT CC CC CC CC CT CT CC CC CC CT CT CC CT CT CC CT CT CC CT CC CC CT CT CT CT CT CC CC CC CC TT TT CT CT CT CC CT CT CT CC CC CT CT CC CC CT CT CT CT CC CC CC TT TT CT TT CT
-rs6694632 A/G chr1 906697 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6694632:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG AG GG AA AG GG GG GG GG AG GG AG GG AG GG GG GG GG AG AG GG AG AG AG AG AG AA AG GG GG GG GG AG AG AG AG GG AG AG AA AG AG AA AG AG AA AG GG GG GG AG GG AG GG AG AG GG GG AG GG GG GG AG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG AA
-rs13303118 G/T chr1 908247 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13303118:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GT GG GT GG GT GG GG GG GG GT GT GG GT GT GG GT GT TT GT GG GG GG GG GT GT GT GT GG GG GT TT GT GT TT GT GT TT GT GG GG GG GG GG GG GG GT GT GG GG GG GG GG GG GT GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GT
-rs2341354 A/G chr1 908436 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2341354:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA GG AG AA GG AG AA AA AA AA AG AA AG AA AG AA AA AA AA AG AG AA AG AG AG GG AG GG AG AA AA AA AA AG AG AG AG AA AG AG GG AG AG GG AG AG GG AG AA AA AA AG AA AG AA AG AG AA AA AG AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA GG
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-rs2341362 C/T chr1 917172 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2341362:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CT CT CC CC CC TT CT CC CT CT TT CT TT CC CT CT CT CT CC CT CC CT CC CC CC CC CC CT CC CT CC CT CT CC CT CC TT TT CC CT CC CC CT CC CC CT CC CT CC CC CC CC CC CC CC CT CC CT CC CC CT CC CC CC CC CT CC CC CC CC CT TT CT CC CT CC CC CC CC CC CT CT CC CC
-rs9777703 C/T chr1 918699 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9777703:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT TT CT CT TT TT TT CC CT TT CT CT CC CT CC TT CT CT CT CT TT CT TT CT TT TT TT TT TT CT TT CT TT CT CT TT CT TT CC CC TT CT TT TT CT TT TT CT TT CT TT TT TT TT TT TT TT CT TT CT TT TT CT TT TT TT TT CT TT TT TT TT CT CC CT TT CT TT TT TT TT TT CT CT TT TT
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-rs1891910 A/G chr1 922320 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1891910:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG AG GG GG GG GG GG GG GG GG AG GG GG GG GG AG AG GG GG GG GG GG AG GG GG AG GG GG AG AG GG GG GG AG AG AG AA GG AG AG GG AG AG GG
-rs9697457 A/G chr1 924208 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9697457:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG
-rs35940137 A/G chr1 930066 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35940137:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs28360890 A/C chr1 930405 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28360890:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs3121567 C/T chr1 933331 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3121567:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CT TT CT CC CC CT TT CT CC CT CT TT CT TT CC CC CT CT CC CT CC CC CT CC CC CC CC CC CT CC CT CC CT CC CC CC CC TT TT CC CT CC CC CC CC CC CT CC CT CC CC CC CT CC CC CC CT CC TT CC CC CT CC CC CC CT CT CC CC CT CT CC CT CT CT CT CC CC CC CC CC CT CT CC CT
-rs3128117 C/T chr1 934427 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128117:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT TT TT CT CT CT CT TT CT CC TT CT TT CT TT CC CT CT CT TT TT CT CT TT TT CT CT TT TT CT CT TT CC CT TT TT TT CT TT TT TT TT TT CT CT CC TT TT CT TT CT CT CT CT CT CT TT CT CC TT CT CC TT TT CT TT TT CT CT CT CT CT CT TT TT CT CT TT CC TT CT CT TT CT CT TT
-rs2465126 A/G chr1 936897 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2465126:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AG GG AG AA AA AG GG AA AA AG AG AG AG AG AA AA AG AG AA AA AA AA AG AG AA AG AA AG GG AA AG AG AG AG AG AA AG GG GG AA AG AG AA AA AG AA AG AA AG AG AG AG AG AG AA AA AG AA GG AG AA GG AG AA AG GG AG AA AA AG AG AA AG GG AG AG GG AA AG AG AG GG AG AG AG
-rs9697358 A/G chr1 937641 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9697358:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AG AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AG AA AA AA AG AG AA AA AG AG AA AA AA AA AA AA AA AA AA AA
-rs2341365 A/G chr1 938555 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2341365:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AG GG AG AA AA AG GG AA AA GG AG AG AG AG AA AA AG AG AA AA AA AA AG AG AA AG AA AA GG AG GG AG AG AG AA AA AA GG GG AA AG GG AA AA AG AG GG AA AG AG AG AG AG AA AA AA AG AA GG AA AA GG AG AA AG GG AG AA AA AG AG AA AG AG AG AG GG AA AG AG AG GG AG AG AG
-rs15842 C/T chr1 938784 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs15842:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CT TT CT CC CC CC TT CC CC CT CT CT CT CT CC CC CT CT CC CC CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CC CC TT TT CC CT CC CC CC CT CC CT CC CC CC CT CC CT CC CC CC CT CC CT CC CC CT CC CC CT CT CT CC CC CT CT CC CT CT CT CT CC CC CC CC CC CT CT CC CT
-rs1126573 A/G chr1 939233 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1126573:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs1891906 A/C chr1 940106 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1891906:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC AC AC AC AC AC AC AC AA AC CC AA AC AA AC AA CC AC AC AC AA AA AC AC AA AA AC AC AA AC AC NN AC CC AC AC AC AA NN AA AA AA AA AC AC AA AA AA AA AC AA CC AC AC AC CC AA AA AC CC AA AC AC AA AA AC AA AA AC AC AC AC AC AC AA AA AC AC AA NN AC CC AC AA AC CC AA
-rs28555183 C/T chr1 946835 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28555183:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC
-rs6657048 C/T chr1 947503 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6657048:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC TT CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs2710888 C/T chr1 949705 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2710888:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CC CT CT CT CT CC CC CC CC CC CC CT CC CC CC CC CT CC CC CT CT CC CC CT CT CC CC CC TT CT CT CC CC CC CC CC CC CT CC CC CT CT CC CC CC CC CT CC CC CC CT CT CC CC CC CC CT CC CC CC CC CC CT CC CC CT CT CT CT CT CT CC CC CT CT CC TT CC CT CT CC CT CT CT
-rs28736676 A/C chr1 963630 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28736676:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs2710875 C/T chr1 967643 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2710875:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CC CC CT CT CT TT CC TT TT CC CT CT CT CT TT CT CT CT CT TT CT TT CT CC CT CT TT CT CT TT CT TT TT TT CT CT CC CC CT TT CT CC TT CC CC CT CC CT CC TT CT CT CT CT TT TT TT TT CT TT CT CC CT CT CC CC CT CT CT CT CT CT CC CT CT CT CC TT CT TT TT CT CT CT CT
-rs9331225 C/T chr1 967909 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9331225:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CT CC CC CC CT CC CC CC CC CC CC CT CT CT CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs3128097 A/G chr1 970323 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128097:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AA AG AG AA AA AA GG AA AA GG AG AG AG AG AA AA AG AA AA AA AA AA AG AA AA AA AA AA AG AA AG AA AA AA AA AA AG AG AG AA AG AG AA AA AA AG GG AA AG AA AG AG AG AA AA AA AA AA AG AA AA AG AG AA AG AA AG AA AA AA AA AA AA AA AA AG AA AA AA AA AA AG AA AA AG
-rs17160776 C/T chr1 975763 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs17160776:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CT CT CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC
-rs9803031 C/T chr1 977063 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9803031:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT CC CT CT TT TT TT CC CC CC CT CC CC CT CC CT CC CT TT CT CT CT TT TT CT CT CT TT TT CC TT CT CT CC CT TT TT CT CC CT TT CT CT TT CC CC TT CT CT CT CC CT CT CT CT CT TT CT CT CC CT CC CC CT CT CC CC CT CT CT CT CT CT CC CT CT CT CT TT CC CT CT CC CT TT CT
-rs13303287 G/T chr1 977533 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13303287:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GT GG GG GG GT GG GG GT GT GT GT GT GG GG GT GG GG GG GG GG GG GG GG GG GG GG GT GG GT GG GG GG GG GG GT GG GG GG GT GT GG GG GG GG GT GG GG GG GG GT GT GG GG GG GG GG GT GG GG GT GT GG GT GT GT GG GG GG GG GG GG GG GG GG GG GG GG GG GG GT GG GG GT
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-rs6667248 A/G chr1 1007079 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6667248:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AA AG AG AA AA AA AA AA AG AG AG AG GG AA AG AG AG AA AA AA AG AA AA AG AG AA AG AA AA AA AG AA AA AG AG AA AA AA AG AA AA AA AA AA AG GG AG AG AA AG AG AA AA AA AG AG AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AG AG AG AG AG AA AA
-rs3766191 C/T chr1 1007450 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3766191:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CT CC CT CT CT CC CT CT CC CC CC CT CC CC CC CC CT CC CC CC CT CC CC CT CT CC CC CT CT CT CT CT CC CC CT CC CC CT CC CC CT CC CC CC CC CC CC CC CT CT CT CC CC CC CC CC CC CC CT CT CC CC CC CC CT CC CT CT CT CT CT CC CT CT CC CC CT CC CT CC CC CC CC CC
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-rs3737728 A/G chr1 1011278 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3737728:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG GG AG GG GG GG AG GG GG GG GG GG AG AG GG AG GG GG AG GG AG GG GG GG AG GG GG GG AG GG AG AG GG AG GG GG AG GG GG GG AG AG AG AG GG GG AG AG AG GG GG AG AG GG GG GG GG GG AG GG GG AG AG AG AG GG AA AG AG AG AG AG AG GG AG AG GG GG GG GG AG AG AG AG AA
-rs9442398 A/G chr1 1011558 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9442398:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG AG AG AG AG AG GG AG AG AG GG GG GG AA AG GG AG GG AA AG GG AG GG GG GG AA AG GG GG AA AG AA AA AG AG GG AG AG AG AG GG AG AA AG AG GG GG AG AG AG AG AG AA AG AG GG GG GG GG AG AA AG AG AG AG AG GG AA AG AG AG AG AG AG AA AG AA GG AG AG AG AG AG AG AG AA
-rs6689308 A/G chr1 1019668 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6689308:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG AG AG GG GG AG AG GG GG AG AG AG AG GG AA AA AA AA AA AG AG AA AG AG GG GG AG GG AG GG AG AG GG AA AG AG AG GG GG AA AG AG AA AG GG GG AG GG GG GG AG AG AA GG AG AA AG AG GG AG GG AA AA AA AA AG AA AG GG AA AA AA AG AA AA AG GG AA GG AG AG GG AG AA AG
-rs6687776 C/T chr1 1020428 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6687776:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT TT CT CT TT TT CC CT TT TT CC CT CT CT TT CC CC CC CC CC CT CT CC CT CT TT TT CT TT CT TT CT CT TT CC CT CT CT TT TT CC CT CT CC CT TT TT CT TT TT TT CT CC CC TT CT CC CT CT TT CT TT CC CC CC CC CT CC CT TT CC CC CC CT CC CC CT TT CC TT CT CT TT CT CC CT
-rs6678318 A/G chr1 1020496 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6678318:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG AA AG AG AA AA GG AG AA AA AG AG AG AG AA GG GG GG GG GG AG AG GG AG AG AA AA AG AA AG AA AG AG AA GG AG AG AG AA AA GG AG AG GG AG AA AA AG AA AA AA AG GG GG AA AG GG AG AG AA AG AA GG GG GG GG AG GG AG AA GG GG GG AG GG GG AG AA GG AA AG AG AA AG GG NN
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-rs6671356 C/T chr1 1029889 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6671356:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CT CT CC TT CT CC CC CT CT CT CT CC TT TT TT TT TT CT CT TT CT CT CC CC CT CC CT CC CT CT CC TT CT CT CT CC CC TT CT CT TT TT CT CC CT CC CC TT TT TT TT CT CT TT CT CT CC TT CT TT TT TT TT CT TT CT CC TT TT TT CT TT TT CT CC TT CC CT CT CT CT TT CT
-rs6604968 A/G chr1 1031563 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6604968:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG AG AG GG AA AG GG GG AG AG AG AG GG AA AA AA AA AA AG AG AA AG AG GG GG AG GG AG GG AG AG GG AA AG AG AG GG GG AA AG AG AA AA AG GG AG GG GG AG AA AA AA AG AG AA AG AG GG AA AG AA AA AA AA AG AA AG GG AA AA AA AG AA AA AG GG AA GG AG AG AG AG AA AG
-rs4970405 A/G chr1 1038818 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4970405:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AG AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG
-rs12726255 A/G chr1 1039813 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12726255:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG AG AG GG AG AG GG GG AG AG AG AG GG AG AG AA AA AA AG AG AA AG AG GG GG AG GG AG GG AG AG GG AA AG AG AG GG GG AA AG AG AA AA AG GG AG GG GG AG AA AG AA AG AG AA AG AG GG AA AG AA AA AA AA GG AA AG GG AG AG AA AG AA AG AG GG AA GG AG AG AG AG AA AG
-rs4970409 A/G chr1 1043315 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4970409:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG AG GG AG AG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG AG AG AG GG GG AG AG GG GG GG GG AG AA GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG GG GG AG GG GG GG GG GG AG
-rs7548798 C/T chr1 1050037 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7548798:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CT CT CC CT CC CT CT CT TT CT CT CC CC CC CC CC CC CT CC CT CC CT CT CC CC CC CC CT CC CC CC CC CC CC CT CC TT CT CC CC CC CC CT CC CT CT CT CC CC CT CC CC CC CC CC CC CC CC CC CT CC CC CC CT CC CT CT CT CC TT CT CT CT CT TT CT CC CC CT CT TT TT TT CT CC
-rs17160824 A/G chr1 1050471 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs17160824:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG AG GG AG AG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG AG AG AG GG GG AG AG GG GG GG GG AG AA GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG GG GG AG GG GG GG GG GG AG
-rs11807848 C/T chr1 1051029 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11807848:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CT CC TT CC CT CC CT CT CC CT CT CT TT CT CT CT TT TT TT CT TT TT CT TT TT TT CT CC CT TT TT CT CT TT CT TT CC CT CC TT TT TT CT TT TT CC CT TT TT CT TT TT TT TT TT TT CT TT TT CT TT TT TT CT TT CT CT CT CT CC CT CT CT CT CC CC TT TT CT TT CC CC CC CT CT
-rs12757754 A/G chr1 1051125 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12757754:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AA AG AA AG AG AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AA AA AG AG AG AA AA AG AG AA AA AA AA AG GG AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AG AA AA AG AA AA AA AA AA AG
-rs9442373 A/C chr1 1052501 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9442373:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC CC AC CC AA CC AC CC CC AC CC AC AC AC CC CC AC AC AA AA AA AC AA AA AC AA AA AA AC CC AC AA AA AC AC AA AC AC CC AC CC AA AC AC AC AA AA CC AC AC AC AC AA AC AA AA AA AA AC AA CC AC AC AA AA AC AA AC AC AC AC CC AC AC AC AC CC CC AC AC AC AC CC CC CC AC AC
-rs2298217 C/T chr1 1054842 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2298217:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CT CC CT CT CC CC CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CC CC CC CT CT CT CC CC CT CT CC CC CC CC CT CT CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CC CC CT CC CC CC CC CC CT
-rs12145826 A/G chr1 1055892 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12145826:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs7520581 G/T chr1 1073862 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7520581:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GT GT GG GG GG GG TT GT GT GG GT GG GG GG GG GG GG GG GG GT GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GT GG GG GT GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GT GG GT GT GG
-rs9442380 C/T chr1 1077546 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9442380:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CT CC CT CT CT CT CC CC CC CT CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CT CC CC CT CT CC CC CT CT CC CT CC CC CC CC CC CC
-rs6686003 A/G chr1 1079562 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6686003:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG AG GG AA AG GG GG AG AA AA AA AG GG AG GG GG AG AG GG AG GG GG AG GG AG AG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG AA AG AG AG AG AG GG GG GG AG AG AG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG
-rs7553429 A/C chr1 1080420 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7553429:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AC AC AA CC AC AA AC AC CC CC CC AC AC CC AA AA AC AC AA AC AA AA AC AA AC AC AA AA AA AC AC AA AA AA AA AA AA AA AA AA AC AC AA AA AA AA AA AA AC CC AC AC AC AC AC AA AA AA CC AC AC AA AA AA AC AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC
-rs4970362 A/G chr1 1084601 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4970362:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG AA AA GG AA AG GG AG AG AA AA AA AA AG AG GG AG AG AA AG GG AG GG AG GG AA AG AG AG GG GG GG GG GG GG GG AG AG AG GG AG GG AA AG AG AG GG GG AG AA AA AG AG AG AA AG GG AA AG AG AG AG AG GG AA AA AG GG AG AG AG GG GG GG AA AG AG GG AG GG GG GG GG GG GG AG
-rs9660710 A/C chr1 1089205 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9660710:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC AC AC AA CC AC CC CC CC CC CC AC CC CC CC CC CC CC CC AC AC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC AC CC CC CC CC CC CC CC AC AC AC CC AC AC CC CC AC CC AC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC CC CC
-rs4970420 A/G chr1 1096336 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4970420:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AG AG GG AA AA AA AA AA AG AA AG AG AA AG AG GG AG AG GG GG AA AA AA GG AG AA AA AA AG AA AG AA AA AG AA AG AG AA GG AG AA AA AG AA AA AA AA AA GG AA AA AA AG AA AA AA AA AA GG GG AG AA AG AA AA AA GG GG AA AA AG GG AG GG AG AA AA AG AG AG AG AA
-rs4442317 C/T chr1 1096647 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4442317:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CT TT TT CT TT TT CC TT TT TT TT CT CT CC CT CT TT TT TT CT TT TT TT CT CT TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT CT CT TT CT TT CC CT CC CC TT CT TT TT TT CT TT CT CT CC TT TT CC CT TT TT CT TT CC CC CT CT CC CT TT CT TT CT TT TT TT TT TT TT TT CT
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-rs11466688 C/T chr1 1130676 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11466688:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
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-rs11466681 C/T chr1 1131250 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11466681:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CT CT CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CC CC NN CC CT CT TT CC TT CC CC CT CC CC CC CC CC CC CC CC CT CT CC CC CT CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC
-rs11466673 C/T chr1 1132188 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11466673:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs11466670 A/G chr1 1132298 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11466670:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs11466668 G/T chr1 1132589 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11466668:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GT GG GG GT GT GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
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-rs34945898 A/G chr1 1136887 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs34945898:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs35569523 A/G chr1 1137518 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35569523:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG AG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG AG GG GG GG AG GG GG GG AG AG AG GG AG AG GG GG GG GG GG GG GG GG AA GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG
-rs35033502 A/G chr1 1138221 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35033502:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG AG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AG AG AG GG
-rs35878953 C/T chr1 1139524 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35878953:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs35222290 C/T chr1 1140718 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35222290:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
-rs11721 A/C chr1 1142494 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11721:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC AA CC AC CC AC AC CC CC AC AA CC AC CC CC CC CC CC CC AC AC CC AC CC CC CC CC CC CC CC AC CC CC AC AA CC AC AC AC CC CC CC CC AC CC CC CC CC CC CC AC AC AC AC CC AC CC CC CC CC CC AC CC AC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC AC AA AC AC AC CC
-rs2887286 C/T chr1 1145994 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2887286:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CC CT CT TT CT CT CT CT CT CT CT CC CT CT TT CT TT CT CT TT CC TT CT CT CC CC TT TT CT CT CT CT CC CT TT CT TT CC CT TT TT TT TT CT CC CT CC CC CT CC CT CT CT CC TT TT TT CT TT CC CC CT CC CT CT CT CC CT CC CT CT TT CT CC CT CT CT CT CC CC CT CT CT TT CC
-rs3813199 A/G chr1 1148140 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3813199:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG GG GG AG AG GG GG AG AA GG AG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG AG AG AG GG GG AG GG GG GG GG GG GG AG AG GG GG GG AG GG GG AG AG GG AG AG AG AG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG AG GG AG AG GG GG GG
-rs6603781 A/G chr1 1148494 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603781:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs6671424 A/G chr1 1150528 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6671424:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG GG GG AG AG GG GG AG AA GG AG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG AG AG AG GG GG AG GG GG GG GG GG GG AG AG GG GG GG AG GG GG AG AG GG AG AG AG AG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG AG GG AG AG GG GG GG
-rs3766186 A/C chr1 1152298 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3766186:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC AC CC CC CC AC AC CC CC AC AC CC AC CC CC CC CC CC CC CC AC CC AC CC CC CC CC CC CC CC CC CC CC CC AC CC AC CC AC AC AC CC CC AC CC AC CC CC CC CC AC AC CC CC CC AC CC CC AC AC CC AC AC AC AC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC AC CC AC AC CC CC CC
-rs7515488 C/T chr1 1153667 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7515488:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CT CT CC CT CT CC CT CC CC CC CC CC CC CC CT CT CT CT CC CC CT CC CC CT CT CT CT TT CC CC CT CC CC CC CC CT CT TT CC TT CT CC CT CC CC CC CT CT CC CC CC CT CT CT CT CT CC CC CT CC CC CC CC CC CC CC CC CC CT CT CC CC CC CT CT CC CC CT CC CT CT CC
-rs11260562 A/G chr1 1155173 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260562:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG AG AG GG AG GG GG GG GG GG GG GG AG GG AG GG GG GG AG GG GG AG AG AG AG AA GG GG AG GG AG GG GG AG AG AA GG AA AG GG AG GG GG GG GG AG GG GG GG AG AG GG GG AG GG GG AG GG GG GG GG GG GG GG GG GG AG AG GG GG GG AG AG GG GG AG GG AG AG GG
-rs7528416 C/T chr1 1161112 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7528416:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT CT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT TT CT CT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
-rs715643 C/T chr1 1162770 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs715643:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC NN CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs6697886 A/G chr1 1163474 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6697886:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AA GG AG GG AG AG AG AG AA AA AG AG GG GG GG AG AG GG AG AG AG AG GG GG AG GG GG AG AG AG AG AA GG AG GG AG AG AG AG AA GG AG AG AG AG GG AG GG GG AG AG AG AG GG AG GG GG AG AG AG AG AG AA AG GG GG GG AG GG GG GG GG AG AG GG GG AG AG AG AG GG AA AG AG AG GG
-rs4970364 C/T chr1 1164145 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4970364:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CT CT CC CT CC CC CC CC CC CC CT CT CT CC TT CC CT CT CC TT CT CC CC CC CT CT CC CT CC CT CC CC CT CT CT CC CC CT CC CT CC CC CC CC CT CT CC CC CC CC CT CC CT CT CT CC CT CC CC CC CT CT CT CT CT CT CT CT CT CT CC CC CT CT CT CT CC CT CC CT CC CT CC
-rs6675798 C/T chr1 1166460 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6675798:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC TT CT TT CT CT CT CT CC CT TT TT TT TT TT CT CT TT TT CT TT CT CT CT TT TT TT CT TT CT CT CC TT CT TT CT CT CT CT CC TT CT CT CT TT TT CT TT TT CT CT CT TT TT CT TT TT TT TT CT CT CT CC CT TT TT TT TT TT TT TT TT TT TT TT TT CT TT CT CT TT CT CT TT TT TT
-rs2297864 A/G chr1 1167493 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2297864:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG AA AG AA AG AG AG AG GG AG AA AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AG AA AG AG GG AA AG AA AG AG AG AG GG AA AG AA AG AA AA AG AA AA AA AG AA AA AA AG AA AA AA AA AG AG AG GG AG AA AA AA AA AA AA AA AA AA AA AA AA AG AA AG AG AA AG AG AA AA AA
-rs11260566 C/T chr1 1168108 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260566:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT CC CT CC CT CT CT CT TT CT CC CC CT CC CT CT CT CC CC CC CC CC CC CC CC CC CC CT CC CT CT TT CC CT CC CT CC CT CC CT CC CT CT CT CC CC CT CC CC CT CT CC CC CC CT CC CC CC CC CT CT CT TT CT CC CC CC CC CC CC CC CC CC CC CC CC CT CC CT CT CC CT TT CC CC CC
-rs12093154 A/G chr1 1168788 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12093154:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG AG GG AG AG GG AG AG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG AG GG AG GG AG GG GG GG GG AG GG GG AG GG AG GG AG GG GG AG AG AG GG AG GG GG GG GG AG GG GG GG AG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG
-rs7541831 A/C chr1 1178043 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7541831:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs3818646 C/T chr1 1181733 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3818646:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC NN CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC NN
-rs7524470 A/G chr1 1182378 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7524470:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG AA AG AA AG AG AG AA AG AG AA AA AG AA AG AG AG AA AA AA AA AA AA AG AA AG AA AA AA AG AG AG AG GG AA AG AG AG AA AA AA AA AG AA AA AG AG AA AA AG AA AG AA AA AG AA AA AA AA AA AG AA AG AG AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AG AG AG AG AG AA AA
-rs12072310 A/C chr1 1183586 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12072310:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC AA AC AA AC AC AC AC CC CC AC AC AC AA AC AC AC AA AA AA AC AA AA AC AC AC AA AC AC CC AC CC AC CC AA AC AC AC AA AC AA AC AC AC AA AC AC AC AC AC AA AC AA AA AC AC AA AA AA AC AC AC CC AC AA AA AA AC AA AA AA AC AA AC AA AA AC CC AC CC AC CC AC CC AC AA
-rs11804831 C/T chr1 1184667 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11804831:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CT CT CC TT CC CT CT CC TT CT CC CC CC CT CT CC CC CC CT CC CT CT CT CT CC CC TT CT CC CT CC CC CC CC CC CC CC CC CC CC CC CT TT TT CT CC CC CC CC CT CT CC CC CC CT CT CT CC CT CC CC CT CT CC CT CC CT CC CC CC CC CC
-rs11260568 C/G chr1 1185553 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260568:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CG GG GG GG GG GG GG GG CG CG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG CG GG CG GG CG GG GG GG GG GG GG GG CG GG CG GG CG GG GG GG CG CG GG GG GG GG GG GG CG GG GG GG CG GG GG CG GG GG GG GG CG GG GG GG GG GG GG GG GG GG CG CG GG GG GG GG GG GG GG
-rs6673601 A/G chr1 1186334 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6673601:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG
-rs6704013 C/T chr1 1187454 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6704013:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CC CC CC CC CC CT CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CT CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CT CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC
-rs12563338 A/T chr1 1188481 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12563338:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT AA AT AA TT AT TT AT TT TT TT TT AT AT TT TT AT TT AT TT TT AT TT TT AT AT AA TT TT TT TT TT TT TT AT TT TT TT AT TT TT TT TT TT AT AT AT AT AT AT AT AT AT AA AT TT TT TT AT TT AT AT TT TT AT AT AT AT AT AT AT AT TT TT AA AT TT TT TT TT TT TT TT TT AT AA
-rs12402622 A/G chr1 1191495 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12402622:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs11260570 C/T chr1 1191503 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260570:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC TT CT TT CT CT CT TT CT CC CT CT CT TT CT CT CT TT TT TT CT TT TT CT CT CT TT TT CT CT CT CT CT CC TT CT CT CT TT TT TT TT CT TT TT CT CT TT TT CT TT CT TT TT CT TT TT TT TT TT CT TT CT CT TT TT TT TT TT TT TT CT TT CT TT TT TT CT TT CT CT CT CT CT TT TT
-rs4018608 C/T chr1 1193801 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4018608:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CC CT CC TT CT TT CT TT TT TT TT CT CT TT TT CT TT CT TT TT CT TT TT CT CT CC TT TT TT TT TT TT TT CT TT TT TT CT TT TT TT TT TT CT CT CT CT CT CT CT CT CT CC CT TT TT TT CT TT CT CT TT TT CT CT CT CT CT CT CT CT TT TT CT CT TT TT TT TT TT TT TT TT CT CC
-rs12073590 A/C chr1 1195018 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12073590:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC CC AA AC AA AC AC AC AA AC AC AA AA AC AA AC AC AC AA AA AA AA AA AA AC AA AC AA AA AA AC AC AC AC CC AA AC AC AC AA AA AA AA AC AA AA AC AA AA AA AC AA AC AA AA AC AA AA AA AA AA AC AA AC AC AA AA AA AA AA AA AA AC AA AC AA AA AA AC AA AC AC AC AC AC AA AA
-rs6667923 A/C chr1 1196206 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6667923:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC AA CC AC CC AC AC AC CC AC AA AC AC AC CC AC AC AC CC CC CC AC CC CC AC AC AC CC CC AC AC AC AC AC AA CC AC AC AC CC CC CC CC CC CC CC AC AC CC CC AC CC AC CC CC AC CC CC CC CC CC AC CC AC AC CC CC CC CC CC CC CC AC CC AC CC CC CC AC CC AC AC AC AC AC CC CC
-rs3737722 A/G chr1 1199499 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3737722:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG AG GG AG AG AG GG AG AG GG AG AG AG GG AA AG AA AG AG AA AA GG GG GG AA AG AG AG AG AG GG AG AG AG AG GG AG AA AA AG AA AG GG GG AG AG GG AG GG AG GG GG AA AA AA AG AA GG GG AG AG AG AG AG AG AG AG AG GG AA AG GG AG AG AG AA GG AG GG AG NN GG GG
-rs11260577 C/T chr1 1200334 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260577:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CT CC CT CC CC CC CT CT CC CT CT CT CC TT CT TT CT CT TT TT CC CC CC CT CT CC CT CC CT CC CT CT CT CT CC CC TT CT CT CT CT CC CC CC CC CC CT CC CC CC CC CT TT TT CT CT CC CC CC CT CT CT CT CC CT CT CT CC TT CT CC CT CT CC CT CC CT CC CT CC CC CC
-rs6689813 C/T chr1 1200826 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6689813:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CC CT CC CT CT CT CC CT CT CT CT TT CT CC TT CT TT CT CT TT TT CC CC CC TT CT CT TT TT CT CC CT CT CT CT CT TT TT TT CT TT CT CT CT CT CT CT CT CT CT CC CC TT TT TT CT TT CC CC CT CT CT CT CT CT CT CT CT CC TT TT CC CT CT CT TT CT TT CC CT CT CC CC
-rs6685064 C/T chr1 1201155 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6685064:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT TT TT TT CT TT CT CT CT TT CT CT TT CT CT CT TT CC CT CC CT CT CC CC TT TT TT CC CT CT CT CT CT TT CT CT CT CT TT CT CC CC CT CC CT TT TT CT CT TT CT TT CT TT TT CC CC CC CT CC TT TT CT CT CT CT CT CT CT CT CT TT CC CT TT CT CT CT CC TT CT TT CT TT TT TT
-rs28488099 A/C chr1 1203168 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28488099:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC AC CC AC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC CC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs3753340 A/G chr1 1206921 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3753340:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG AG AG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AA GG AG AG AG GG GG GG GG GG AG GG AG GG AG GG GG AG AA AG GG GG GG GG GG GG AG GG GG GG AG AG AG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG
-rs6661354 A/G chr1 1207869 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6661354:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs6603788 C/T chr1 1207949 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603788:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT CT TT CT TT TT TT CT CT TT CT CT CT TT CC CT CC CT CT CC CC TT TT TT CT CT TT CT TT CT TT CT CT CT CT TT TT CC CT CT CT CT TT TT TT TT TT CT TT TT TT TT CT CC CC CT CT TT TT TT CT CT CT CT TT CT CT CT TT CC CT TT CT CT TT CT TT CT TT CT TT TT TT
-rs12076303 C/T chr1 1208663 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12076303:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
-rs12077700 C/T chr1 1209638 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12077700:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CT CC CT CC CC CC CC CC CC CC CT CC CT CC CT CC CC CT TT CT CC CC CC CC CC CC CT CC CC CC CT CT TT CT CC CC CC CC CT CC CC CC CC CC CC CC CC CT CT TT CT CT CC CC CC CT CC
-rs2144440 A/G chr1 1209999 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2144440:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG AG GG AG GG AG GG AG AG GG AG AG AG GG AA GG AA AG AG AA AA GG GG GG AG AG GG AG GG AG GG AG AG AG AG GG GG AA AG AG AG GG GG AG GG GG GG AG GG GG GG GG AG AA AA AG AG GG GG GG AG AG AG AG GG AG AG AG AG AG GG GG AG AG GG AG GG AG GG AG GG GG GG
-rs6662635 A/G chr1 1210288 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6662635:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AA AA AA AA AA AA AA AG AG AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AG AA AG AA AG AA AA AA AA AA AA AA AG AA AG AA AG AG AA AG GG AG AA AA AA AA AA AA AG AA AA AA AG AG AG AG AA AA AA AA AG AA AA AA AA AG AG AA AA AA AG AG AA AA AA AA AA AA AA
-rs3737721 A/G chr1 1217760 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3737721:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AG AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AG AA AG AG AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AG AG AA AA AG AG AG AA AA AA AA AA AA AA AA AA AA AA AG AA AG AG AG GG AA AA AA AG AA AA AA AA AA AA AA AA AA AG
-rs35134975 A/G chr1 1219306 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35134975:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs6669227 C/T chr1 1219633 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6669227:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT TT TT TT TT TT TT TT TT TT TT TT CT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT TT CT TT TT CT TT CT CT TT TT TT TT TT CT TT TT TT CT TT CT TT TT TT TT TT TT TT TT CT CT CT CT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT CC CT CT CC CT TT TT
-rs1749951 A/G chr1 1221519 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1749951:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs604618 A/G chr1 1222182 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs604618:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AG AA AA AG AG AG AG AA AG AA AG AA AG AG AG AA GG AG GG GG AG GG GG AA AG AG AG AG AG AA AA GG AG AG GG AG AG AA AA GG AG AA GG AA AA AA AA AG AG AA AA AG GG AG AG GG GG AG AA AA AA AA AG AG AA AG AA GG GG GG GG AG AA AA GG AG AA GG AA AG AG AA AG GG AG
-rs1739855 C/T chr1 1223804 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1739855:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CT CT CT CC CC CC CC CC CC CT CT CT CC TT CC TT TT CT TT CT CC CC CC CT CT CT CC CC TT CT CT CT CT CC CC CC TT CT CC TT CC CC CC CC CC CC CC CC CC CT CC CT TT TT CT CC CC CC CC CT CT CC CC CC CT CT CT CC CT CC CC CT CT CC TT CC CT CT CC CT TT CC
-rs2477782 C/T chr1 1226899 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2477782:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CT CT CT CC CC CC CC CC CC CT CT CT CC TT CC TT TT CT TT CT CC CC CC CT CT CT CC CC TT CT CT CT CT CC CC CC TT CT CC TT CC CC CC CC CC CC CC CC CC CT CC CT TT TT CT CC CC CC CC CT CT CC CC CC CT CT CT CC CT CC CC CT CT CC TT CC CT CT CC CT TT CC
-rs11586188 A/G chr1 1227692 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11586188:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG NN GG GG GG GG GG GG GG GG NN AG AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG NN GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG
-rs11260584 G/T chr1 1229202 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260584:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT GT TT TT GT GT GT GT TT TT TT TT TT GT GT GT TT GG GT GG GG GT GG GG TT GT GT GT GT GT TT TT GG GT GT GG GT GT TT TT GG GT TT GG TT TT TT TT GT GT TT TT GT GT GT GT GG GG GT TT TT TT TT GT GT TT TT TT GG GG GT TT GT TT TT GT GT TT GG TT GT GT TT GT GT GT
-rs12410087 A/C chr1 1229798 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12410087:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA NN AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AA AA AA AA AA AA
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-rs1536167 A/G chr1 1230886 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1536167:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AG AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AG AA AG AG AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AG AG AA AA AG AG AG AA AA AA AA AA AA AA AA AA AA AA AA AA AG AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG
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-rs3737717 A/G chr1 1231947 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3737717:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AG AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AG AA AG AG AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AG AG AG AA AA AG AG AG AA AA AA AA AA AA AA AA AA AA AA AA AA AG AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG
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-rs11801967 C/T chr1 1245896 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11801967:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CT TT TT CT CT CT CC CT TT CC CT CT CT CC CC CT CC CC CC CC CT CC CC CT CT CT CC CC CC CT CC CC CC CT CC CC CC CT CC CC CC CT CC TT CT CC CC CC CC TT CT CT CC CT CC CC CC CC CT CC CC CC CC CT TT TT CT CC CC CT CT CT CT TT CT CT CC CC CC CC CC CC CC CC CT
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-rs3845293 A/C chr1 1248109 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3845293:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AC AA AA AC AC AC AC AA AA AA AA AA AC AC AC AA CC AC CC CC AC CC CC AA AC AC AC AC AC AA AA CC AC AC CC AC CC AA AA CC AC AA CC AA AA AA AA AC AC AA AA AC AC AC AC CC CC AC AA AA AC AA AC AC AA AA AA CC CC AC AA AC AA AA AC AC AA CC AC AC AC AA AC AC AC
-rs167405 A/G chr1 1249647 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs167405:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs35913253 A/G chr1 1259642 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35913253:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs35424002 A/G chr1 1259849 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35424002:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG AG AG GG GG AG AG AA AA AG AG GG GG GG GG AG GG AG GG GG GG GG GG AG AG GG AG AG AG GG AG GG GG GG GG GG GG GG AG GG AG GG GG GG GG AA AA AG GG AG GG AG AG AG AG GG GG AG AG AG AG AG GG GG GG AG AG GG GG AG AG GG GG GG AG AG AA GG GG GG GG GG GG AG GG
-rs28475450 A/G chr1 1264213 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28475450:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG AG AG GG GG AG AG AA AA AA AA GG GG GG GG GG GG AG GG GG GG GG GG AG AG GG AG AG AG GG AG GG GG GG GG GG GG GG AG GG AG GG GG GG GG AA AA AG GG AG GG AG AG AG AG GG GG AG AG AG AG AG GG GG GG AG AG GG GG AG AG GG GG GG AG AG AA GG GG GG GG GG GG AG GG
-rs3855955 A/G chr1 1265940 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3855955:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG AG GG AG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs17854636 C/T chr1 1267396 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs17854636:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs182532 C/T chr1 1276903 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs182532:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs307380 A/G chr1 1276990 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs307380:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG AA AG AG AA AA AG AG GG GG GG GG AA AA AA AA AA AA AG AA AA AA AA AA AG AG AA AG AG AG AA AG AA AA AA AA AA AA AA AG AA AG AA AA AA AA GG GG AG AA AG AA AG AG AG AG AA AA AG AG AG AG AG AA AA AA AG AG AA AA AG AG AA AA AA AG AG GG AA AA AA AA AA AA AG AA
-rs34389364 A/G chr1 1285186 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs34389364:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG GG GG GG GG AG AG GG GG GG GG GG AG AG AG GG AA AG AA AA AG AA AA GG AG AG AG AG AG GG GG AA AG AG AA AG AA GG GG AA AG GG AA GG GG GG GG AG AG GG GG GG AG AG AG AA AA AG GG GG AG GG AG AG GG GG GG AA AA AG GG AG GG GG AG AG GG AA AG AG GG GG GG GG AG
-rs34876581 C/T chr1 1285266 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs34876581:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CT TT TT CT CT CT CT TT TT TT TT TT CT CT CT TT CC CT CC CC CT CC CC TT CT CT CT CT CT TT TT CC CT CT CC CT CC TT TT CC CT TT CC TT TT TT TT CT CT TT TT TT CT CC CT CC CC CT TT TT CT TT CT CT TT TT TT CC CC CT TT CT TT TT CT CT TT CC CT CT TT TT TT TT CT
-rs2765023 C/T chr1 1286928 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2765023:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT TT CT CT CT CT CC CT CC CC CC NN CT CT CC CT TT CC CT CT CC TT CC CT CT TT TT CC CC CC CT CC CC CT CT CT CC CT CT CC CC CC TT CC TT CT CC CC CT CT CT CT CT CT CT CC CC CC CC CT CT CT CT CT CT TT CT CT CT CT CC CT CT CT TT CC CC CC CT CT CC TT CT CT CT TT
-rs2765022 C/T chr1 1286934 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2765022:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs2765021 C/T chr1 1287285 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2765021:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT TT CT CT TT TT CT CT CC CC CC NN TT TT TT TT TT TT CT TT TT TT TT TT CT TT TT CT CT CT TT CT TT TT TT TT TT TT TT CT TT CT TT TT TT TT CC CC CT TT CT TT CT CT CT CT TT TT CT CT CT CT CT TT TT TT CT CT TT TT CT CT TT TT TT CT CT CC TT TT TT TT TT TT CT TT
-rs34186100 C/T chr1 1291496 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs34186100:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
-rs17160669 C/T chr1 1295424 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs17160669:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CT CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CT CT CC CT CC CT CC CT CT CC CC CC CT CT CC CC CC CT CC CT CC CC CC CC CC CC CC CT CC CC CT CT CC CC CC CT TT CC CC CC CC CC CC CT CC CC CC CC CC CC CT CT CC CC CC CT CC CC CC CC CT TT CT CC CC CT CC CT
-rs2765015 A/G chr1 1298845 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2765015:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs2765036 A/G chr1 1299840 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2765036:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs2765033 C/T chr1 1300787 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2765033:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs2649589 A/G chr1 1301579 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2649589:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG AG GG GG AG AG AG AG GG GG GG GG AG AG AA AA AG AA AG AA AA AG AA AA GG GG GG AG AG AG AG AA AG AG AG AA AA AA AG AG AA AG GG AA GG AG GG GG AG AA GG AG GG AG AG AG AA AA AG GG AG AG AG AA AG GG GG GG AA AA AG AG AG AG GG AG AA GG AA AA AA AG AG AG GG AG
-rs2649588 C/T chr1 1303878 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2649588:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT TT CT CT TT TT CT CT CC CC CC CC TT TT TT TT TT TT CT TT TT TT TT TT CT CT CT CT CT CT TT TT CT CT TT TT TT TT TT CT TT CT CT TT TT TT CC CC CT TT CT TT CC CT CT CT TT TT CT CT CT CT TT TT TT TT CT CT TT TT CT CT TT TT TT CT TT CC TT TT TT CT CT CT CC TT
-rs2477777 C/T chr1 1304035 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2477777:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT TT CT CT TT TT CT CT CC CC CC CC TT TT TT TT TT TT CT TT TT TT TT TT CT CT CT CT CT CT TT TT CT CT TT TT TT TT TT CT TT CT CT TT TT TT CC CC CT TT CT TT CC CT CT CT TT TT CT CT CT CT TT TT TT TT CT CT TT TT CT CT TT TT TT CT TT CC TT TT TT CT CT CT CC TT
-rs1240743 A/C chr1 1323299 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1240743:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AC AA AA AA AA AA AA AA AA AC AA AC AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AC AC AC AA AA AC AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA CC AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs35242196 A/C chr1 1323461 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35242196:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC AC CC AC CC AC CC CC CC CC CC CC CC CC CC AC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC AC AC CC CC CC CC CC AC
-rs2291889 A/G chr1 1325081 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2291889:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs1240707 C/T chr1 1325165 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1240707:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CT CT CT CC CC CT TT TT TT TT TT CT CC CT CC CC CC CT CC CC CC CC CC CT CT CT CT CT CT CC CC CT CT CC CC CC CC CC CC CC CT CT CC CC CC TT TT TT TT CT CC CT CT CT CT CC CC CT CT CT CT CC CC CC CC CT CT CT CT CT CT CC CC CC CT CC TT CC CC CC CT CT CT TT CC
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-rs12032637 A/G chr1 1455245 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12032637:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG AG GG GG AG GG GG GG AG GG GG AA AG AG GG AA GG AA AA AG AA AG GG GG GG AG AG AG GG GG AA AG AA AG AG AG GG AG AA AG GG AA AG GG GG GG GG GG GG GG GG GG GG AG AA AA AG GG AG AA AG AG AG GG AG GG AG AG AG GG AA AG GG AG AG GG AG AG AG AG AG GG GG GG
-rs6683520 C/T chr1 1456691 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6683520:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT TT TT CC TT CT CT TT TT TT CT TT TT CC CT CC CT CC TT CC CC CC CC CT TT TT TT CT CT CT TT TT CC CT CC CT CT CT TT CT CC CT TT CC TT TT TT TT TT TT TT TT TT TT TT CT CC CC CT TT CT CC CT CT CT TT CT TT CT CT CT TT CC CT TT CT CT TT CT CT CT CT CT TT TT TT
-rs1987191 C/T chr1 1457348 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1987191:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC TT CC CT CT CC CC CC CT CC CC TT CT TT CT TT CC TT TT TT TT CT CC CC CC CT CT CT CC CC TT CT TT CT CT CT CC CT TT CT CC TT CC CC CC CC CC CC CC CC CC CC CC CT TT TT CT CC CT TT CT CT CT CC CT CC CT CT CT CC TT CT CC CT CT CC CT CT CT CT CT CC CC CC
-rs3118505 C/T chr1 1461910 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3118505:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC
-rs9782908 C/T chr1 1462064 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9782908:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs1571149 A/G chr1 1464030 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1571149:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG GG GG GG GG GG GG AG AG GG AG AG AG GG AA GG GG AG GG AA AG GG GG GG AG AG GG GG GG AG GG AG AG AG AG GG AG AA AG GG AA GG GG GG GG GG GG GG GG GG GG GG AG AG AA AG GG GG GG GG AG AG GG GG GG GG GG AG GG GG GG GG AG AG GG AG GG GG GG GG GG GG GG
-rs1571150 A/C chr1 1464167 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1571150:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC AA AC AC AA AA AA AC AA AA AC AC AC AA AC AC AC AA CC AA AA AC AA CC CC CC AA AC AC CC AC CC CC AC AC AC CC CC CC AC AC CC CC AA CC AC AC AA AC AC AA AC AC AC AA AA CC AC AC AA AA AA AA AA AC CC AC AA CC AC AC AC AC AA AA AC AC AC CC CC AC AC AC AC AC AC AC
-rs1046878 A/G chr1 1466971 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1046878:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG AG GG GG AG GG GG GG GG AG GG GG AG GG GG AG AG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG AG AG GG AG GG GG GG GG GG GG AG GG AG GG GG GG GG AG
-rs7290 C/T chr1 1467107 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7290:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CC CC CC CC CC CC CC CT CT CC CT CT CT CC TT CC CT TT CC TT CT CC CC CC CT CT CC CC CC CT CC CT CT CT CT CC CT TT CT CC TT CC CC CC CC CC CC CC CC CC CC CC CT CT TT CT CC CC CC CC CT CT CC CC CC CC CC CT CC CC CC CC CT CT CC CT CC CC CC CC CC CC CC
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-rs3766180 C/T chr1 1468016 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3766180:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CC CC CC CC CC CC CC CT CT CC CT CT CT CC TT CC CT TT CC TT CT CC CC CC CT CT CC CC CC CT CC CT CT CT CT CC CT TT CT CC TT CC CC CC CC CC CC CC CC CC CC CC CT CT TT CT CC CC CC CC CT CT CC CC CC CC CC CT CC CC CC CC CT CT CC CT CC CC CC CC CC CC CC
-rs3766178 C/T chr1 1468043 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3766178:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CC CC CC CC CC CC CC CT CT CC CT CT CT CC TT CC CT TT CC TT CT CC CC CC CT CT CC CC CC CT CC CT CT CT CT CC CT TT CT CC TT CC CC CC CC CC CC CC CC CC CC CC CT CT TT CT CC CC CC CC CT CT CC CC CC CC CC CT CC CC CC CC CT CT CC CT CC CC CC CC CC CC CC
-rs7517401 A/G chr1 1472873 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7517401:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AA AA AA AG AA AG AA AA AA AA AG AG AA AG AG GG AG GG AA AA AG AG GG GG AG AA AG AG AG AG AG GG AG AA AG GG AG GG AA AG GG AG AA GG AA AA AA AG AA AA AA AA AA AA AA AG AG GG AG AA AA AA AA AG AG AA AA AG AA AA AG AA AA AA AA AG AG AA AG AA AA AG AG AG AG AA
-rs12089738 C/T chr1 1473347 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12089738:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs2031709 A/C chr1 1475847 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2031709:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC AC CC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC CC CC CC CC AC CC CC AC CC CC CC CC AC CC CC AC CC CC AC AC CC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC CC AC AC CC AC CC CC CC CC CC CC AC CC AC CC CC CC CC AC
-rs3128342 A/C chr1 1476697 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128342:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AC AC AA AA AA AC AA AC AA AC CC AA AC AA AA AA AA AC AC AA AA AA AC AA AC AC AC AC AA AC CC AC AA CC AA AA AA AA AA AA AA AA AA AA AA AC AC CC AC AA AA AA AA AC AC AA AA AA AA AA AC AA AA AA AA AC AC AA AA AA AA AA AA AA AA AA
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-rs6603790 C/T chr1 1478446 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603790:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CC CC CC TT CT CC CC CT CT CC CT TT CC CT CC CC CC CT CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CT CT CT CT TT CC CC CT CT CT CC CC CC CT CC CT CC CT CT CC CT CT CC CC CC CT CT CC CT CC CT CT CC CC CC CC CC CC CT CT CC
-rs7531530 C/T chr1 1479533 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7531530:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT CC CT TT TT TT TT TT TT TT CT CT TT CT CT CT TT CC TT TT CT TT CC CC CT CT CT CC CT CT CT CC CT TT CT CC CC CC TT CT CC CT TT CC CT TT CT TT TT TT CC CT CT TT CT CT CT CC CT TT TT TT TT CT CT CT TT CT TT TT CT TT TT TT CC CT CT CT CT CT TT CT CT CT CT TT
-rs3820075 A/G chr1 1480422 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3820075:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG AA AG AG GG AG AG GG GG GG AG AG GG AG AG AA AG AA GG GG AG AG AA AA AG AG AG AA AG AG AG AA AG GG AG AG AA AG GG AG AA AG GG AA AG GG AG AG GG GG AA AG AG GG AG AG AG AA AG GG GG GG GG AG AG GG GG AA GG GG AG GG GG GG AA AG AG AG AG AG GG AG GG AG AG GG
-rs1926883 A/G chr1 1482130 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1926883:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs2377417 A/G chr1 1484510 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2377417:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG
-rs3766170 C/T chr1 1486871 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3766170:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CC CC CC CC CC CC CC CT CT CC CT CT CT CC TT CC CC CT CC TT CT CC CC CC CT CT CC CC CC CT CC CT CT CT CT CC CT TT CT CC TT CC CC CC CC CC CC CC CC CC CC CC CT CT TT CT CC CC CC CC CT CT CC CC CC CC CC CT CC CC CC CC CT CT CC CT CC CC CC CC CC CC CC
-rs3766169 A/C chr1 1487064 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3766169:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC CC CC CC CC CC CC CC CC CC CC AC AC CC AC AC AC CC AA CC AC AA CC AA AC CC CC CC AC AC CC CC CC AC CC AC AC AC AC CC AC AA AC CC AA CC CC CC CC CC CC CC CC CC CC CC AC AC AA AC CC CC CC CC AC AC CC CC CC CC CC AC CC CC CC CC AC AC CC AC CC CC CC CC CC CC CC
-rs2296716 C/T chr1 1487687 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2296716:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs2296715 C/T chr1 1488015 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2296715:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CT CC CC CC CC CT CC CC CT CC CC CT CT CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CT CT CC CT CC CC CC CC CC CC CT CC CT CC CC CC CC CT
-rs11260611 C/T chr1 1488240 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260611:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CT CC CC CC CC CT CC CC CT CC CC CT CT CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CT CT CT CC CT CC CC CC CC CC CC CT CC CT CC CC CC CC CT
-rs9439468 A/G chr1 1489161 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9439468:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG GG GG GG GG GG GG AG AG GG AG AG AG GG AA GG GG AG GG AA AG GG GG GG AG AG GG GG GG AG GG AG AG AG AG GG AG AA AG GG AA GG GG GG GG GG GG GG GG GG GG GG AG AG AA AG GG GG GG GG AG AG GG GG GG GG GG AG GG GG GG GG AG AG GG AG GG GG GG GG GG GG GG
-rs6603791 A/G chr1 1490804 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603791:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG GG GG GG GG GG GG AG AG GG AG AG AG GG AA GG GG AG GG AA AG GG GG GG AG AG GG GG GG AG GG AG AG AG AG GG AG AA AG GG AA GG GG GG GG GG GG GG GG GG GG GG AG AG AA AG GG GG GG GG AG AG GG GG GG GG GG AG GG GG GG GG AG AG GG AG GG GG GG GG GG GG GG
-rs6603793 C/T chr1 1495118 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603793:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT TT TT TT TT TT TT TT TT TT CT CT TT CT CT CT TT CC TT TT CT TT CC CT TT TT TT CT CT TT TT TT CT TT CT CT CT CT TT CT CC CT TT CC TT TT TT TT TT TT TT TT TT TT TT CT CT CC CT TT TT TT TT CT CT TT TT TT TT TT CT TT TT TT TT CT CT TT CT TT TT TT TT TT TT TT
-rs7516244 A/C chr1 1499328 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7516244:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs7519837 C/T chr1 1500664 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7519837:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT TT TT TT TT TT CT CT TT TT CT CT TT CT CT CT TT CC TT TT CT TT CC CT TT TT TT CT CT TT TT TT CT TT CT CT CT CT TT CT CC CT TT CC TT TT TT TT TT TT TT TT TT TT TT CT CT CC CT TT TT TT TT CT CT TT TT TT TT TT CT TT TT TT TT CT CT TT CT TT TT TT TT TT TT TT
-rs6687029 A/C chr1 1508931 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6687029:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC CC AA AC AA AA AA AC AA AC AC AC AC AA AC AC CC CC CC AA AC AC AA AC AC AC AA AA AC AA AC AC AA AC CC AA AC AC AA AA AA AC AC AA AC AA AA AC AA AA AC AC AA CC AA AA AC AC AC AC AA AA AA AC AA AC AA AC AA AA AA AC AC AA AA AC AC AC AA AA AA AA AA AA AA AC AA
-rs6604983 A/G chr1 1511458 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6604983:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AG
-rs4648786 C/T chr1 1511668 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648786:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT CT TT CT TT TT CT CT TT CT CC TT CT CT CT TT CT CT CC CT CC CT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT CT CT CT CC CT CT CT TT TT CT TT CT TT TT TT CT CT CT CC CT TT TT TT TT CT CT TT CT TT TT TT CC CT TT TT TT CC CC CT TT TT TT CT CT TT TT TT
-rs28414855 A/C chr1 1516133 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28414855:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs35945226 A/G chr1 1523269 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35945226:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs11552172 C/T chr1 1524477 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11552172:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CT CT TT CT CT TT CT TT TT TT TT TT CT CT CT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT CT CT CT TT TT CT TT CT TT TT TT TT CT CT TT CT TT TT TT TT TT CT TT TT TT TT TT CC CT TT TT TT CC TT TT TT TT TT TT CT TT TT TT TT CC CT TT TT TT TT CT
-rs4648782 A/G chr1 1532049 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648782:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG AG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG AG AG GG GG GG GG GG GG GG AA AG AG AA GG
-rs28430872 A/G chr1 1539468 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28430872:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG AG GG AG AG GG AG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG AG AG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG AA GG GG GG GG GG GG GG GG GG GG GG AA AG GG GG GG GG GG
-rs4648611 A/G chr1 1540565 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648611:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AA AG GG AG AG GG AG AG GG GG GG AA AG AA AG AG GG AG GG GG GG AG GG GG AG GG AG AG AG GG GG AG AA AG AG AG AG GG GG AG GG AG GG AG GG AG AA AG GG AA AA GG GG AG AG AG GG GG AG GG AG AA AG GG GG GG AG AG AG GG GG GG GG AG GG AG AA AG AA AA GG AG GG GG AG
-rs12748433 A/G chr1 1549834 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12748433:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AG AA AG AA AG AA AA AA GG AA AG AA AA AA AA AG AA AG AA AA AG AA AA AA AG AA AG AG AG AA AA AG AG AA AA AA AA AG AA AA AA AA AA AG GG AA AA AA AA AA AG AA AA AA AA AA AA AG AG AA AA AA AA AG GG AG AA AA AA AA AA AG AG AG AA AA AA AA AA AA AG AG AA AG AA
-rs28635343 A/G chr1 1549966 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28635343:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG AG GG AG AG GG AG GG GG GG GG GG AG AG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG AG AG AG GG GG GG GG AG GG GG GG GG AG AG GG AG GG GG GG GG GG AG GG GG GG GG GG AA AG GG GG GG AA GG GG GG GG GG GG GG GG GG GG GG AA AG GG GG GG GG AG
-rs28464684 A/G chr1 1556023 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28464684:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AG GG GG GG AG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG
-rs28456011 C/T chr1 1557069 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28456011:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CT CT CC CT CT CT CT CT CC CC CC CC CT CT CT CT CC CC CC CC CC CC CT CT CT TT CC CC CC CC CC CC CT CT CC CT CC CC CC CC CC TT CC CC CC CC CT CT CC CT CC TT CC CC CC CT CC CC CC CT CC TT CT CC CC CC TT CC CC CC CC CC CC CC CC CC CC CC TT CT CC CC CC CC CC
-rs35154105 A/G chr1 1588771 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35154105:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs6604981 C/T chr1 1589024 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6604981:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CC CC CC CT CC CC CT CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC
-rs4639697 G/T chr1 1592650 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4639697:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs6699975 A/C chr1 1593297 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6699975:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC AC CC AC AC CC CC CC AC AC CC CC CC AC CC AC CC AC AC AC AC AC CC CC CC CC CC CC CC CC AC CC AC AA AC AA CC CC AA AC CC AA CC CC AC CC CC CC CC CC CC CC CC AC AC AA AC CC CC CC CC CC CC CC CC CC AA AC CC CC AC CC CC CC CC CC AA CC AC CC CC CC CC CC
-rs28707307 C/T chr1 1600672 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28707307:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT CT TT CC CT TT
-rs4074196 C/T chr1 1601858 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4074196:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT CC CT CC TT CT CC CC CC CT TT CT CT TT TT CT CT TT CT TT CT CT TT CT TT CT CT CT CC CC CT CC CC CC TT CT CT CT TT CT CC CT CT CT CT CT CT CC CC CC CT TT CT CT CT CC CC CT TT CT CT TT TT CT CT TT TT CT CT CT TT CC CT CT CT TT CT TT CC CC CC TT CT TT TT CT
-rs4074197 A/G chr1 1601974 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4074197:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AA AA AA AA AG AA AA AA AA AA AG AG AA AG AA AG AA AG AA GG AG AG AG AG AG AG AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AG AA AG AA AA AG AA AA AA AA AG AG AA AG AA AA AG AG AG AA AA AA AA AA AA AA AA AG AG GG AA AG AA AG GG AG AG AA AA AA AA AA AA AA AG
-rs7520934 G/T chr1 1605211 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7520934:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GT GT GG GG GG TT GT GG GG GG GG GT GT GG GT GT GT GG TT GT TT GT GT TT GT TT GT GT GT GG GG GG GG GG GG GT GG GT GG GT GG GG GT GT GT GT GT GT GG GG GG GT TT GT GT GT GG GG GT GT GG GT TT GT GG GT GT GG GT GT GT TT GG GT GT GG TT GT TT GG GG GG GT GT GT GG GG
-rs28487995 C/T chr1 1609404 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28487995:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT TT CT CT CT TT CC TT TT CT CC CT CT CT CT CT CT CT TT CT CC TT CC CT CC CT CT CT CT TT CT TT TT TT CC CT TT CC CT CT CC CC CT CC TT CT CT TT CT CT TT CT CT CT CT CC CC CC CC CT CC CC CC CC CT CT CC TT CT CT CC CC CT CT CT CC CT CT CT TT TT TT TT CT CT CC
-rs9442426 C/T chr1 1615647 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9442426:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
-rs760925 A/G chr1 1636434 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs760925:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA GG AG AG AA AA AG GG GG AG AG GG GG AG AG GG GG AG AG GG GG AG AG GG AA AG AG GG GG GG AA AG GG AG AG GG AG AG AG GG GG AG AG GG AG AG GG GG GG GG AG NN AG AG AG AG GG GG GG GG AA AA AA AG AG AA AG AG GG GG GG GG GG AG GG GG GG AG GG GG GG AG AG AG GG AG
-rs909823 A/C chr1 1637546 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs909823:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA CC AC AC AA AA AC CC CC AC AC CC CC AC AC CC AC AC AC CC CC AC AC CC AA AC AC CC CC CC AA AC CC AC AC CC AC AC AC CC CC AC AC CC AC AC CC CC CC CC AC AA AC AC AC AC CC CC CC CC AA AA AA AC AC AA AA AC CC CC CC CC CC AC CC CC CC AC CC CC CC AC AA AC CC AC
-rs2294489 C/T chr1 1653984 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2294489:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT CT TT TT TT CC CT TT TT TT CT CT CT CT CT CC TT CT CT TT TT TT CC CT TT CC CT CT TT CT CC CT CT TT CT CC CT TT CC TT TT CT CT TT TT TT TT TT TT TT CT CC CC CC TT TT TT TT CT CT TT CC CT CC CC CC TT CT TT TT CC CT TT CC TT CT TT TT TT TT CT
-rs4648764 C/T chr1 1655473 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648764:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT CT TT TT CT CT TT CT CT TT TT TT TT TT TT CC CT TT TT CT CT TT CT TT TT TT TT TT CT TT TT CT TT TT TT TT TT TT TT TT TT CT CT CC TT TT TT TT CT CT TT CT TT CT CT CT TT CT TT TT CT CT TT CT TT TT TT TT TT TT TT
-rs7407 C/T chr1 1674332 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7407:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CT CC CT CT CC CT CC CC CC CC CC CC TT CT CC CC CC CT CC CC CT CT CC CC CT TT CT CC CT CC CC CC CT CC CC CC CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CT
-rs34306661 C/T chr1 1677485 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs34306661:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CT TT CT TT TT TT TT CT TT CT TT CT TT CT TT CT TT TT CT CT TT CT CT TT CT CT TT TT TT CT TT TT TT CT TT TT TT TT TT TT TT TT CT CT TT CT TT CT CC TT TT CT TT TT TT TT CT CT CT CT CT TT CT CT TT CT TT CT CT CT TT CT TT TT CT CT TT CT TT TT TT TT TT TT TT
-rs2281173 A/G chr1 1678052 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2281173:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AG AA AG AA AA AA AA AG AA GG AG AA AA AA AG AG AG AG AG GG AA AG AG AA AG AG GG AG AA GG AG AG AA AG GG AG AG AA AG GG AG AA GG AG AA AG AG AG GG AA AA AG AA AA AG GG GG GG AG AA AA AA AG AG AA GG AG GG GG GG AG AG AA AA GG AG AA GG AA AG AA AA AA AA AG
-rs2235536 C/T chr1 1679024 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2235536:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CT CC CC CT CT CC CT CT CC CC CC CC CC CC CT CC CC CC CT CC CC CC CC CC CC CC CC CT CC CC CT CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CT CT CC CT CC CT CT CT CC CT CC CC CT CT CC CT CC CC CC CC CC CC CC
-rs2235537 C/T chr1 1679622 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2235537:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT TT TT CC CT CC TT TT CT TT CT TT TT CT CT TT CT CT CT CT CT CT CT CT CT CT CC TT CT TT CC CT TT CT CT CT CT CT CC CT TT TT TT CT CT CT CT TT CT CT CT CT CT CT CT TT TT CT CC TT TT TT TT CT CC CT CT CT CT CT CT TT CT CT TT CT CT TT CT TT TT TT TT CT TT TT
-rs35672141 C/T chr1 1680910 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35672141:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CT CC CT CT CC CT CC CC CC CC CC CC TT CT CC CC CC CT CC CC CT CT CC CC CT TT CT CC CT CC CC CC CT CC CC CC CC CC CC CC CT TT CT CC CC CC CC CC CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CT
-rs1107910 C/T chr1 1682181 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1107910:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT TT TT CT CT CC TT TT TT TT TT TT TT CT CT TT TT CT CT CT CT CT CT CT CT TT CT TT CT TT CT CT TT CT CT CT CT CT CC CT TT TT TT CT CC CT CT TT TT TT CT CT TT CT CT TT TT CT CC TT CT TT TT CT CC CT CT CT CT CT CT TT CT CT TT CT CT TT CT TT TT TT TT CT TT TT
-rs876029 G/T chr1 1685434 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs876029:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GT GT GG TT GT TT GT GG GT GG TT GT GT GT TT GT GT TT TT GT TT GT GT GT GT GT TT TT TT GG TT GT GT GT GT TT TT TT TT TT TT GT GG TT TT GT TT TT GT TT TT GT GT GT GT GT TT TT TT GT TT GT GG GT TT GT TT TT TT TT TT GT GT GT GG TT GT GG TT GG GT GG GG GT GG GT
-rs5021859 C/T chr1 1686519 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs5021859:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CT TT CC CT CC CT TT CT TT CC CT CT CT CC CT CT CC CC CT CC CT CT CT CT CT CC CC CC TT CC CT CT CT CT CC CC CC CC CC CC CT TT CC CC CT CC CC CT CC CC CT CT CT CT CT CC CC CC CT CC CT TT CT CC CT CC CC CC CC CC CT CT CT TT CC CT TT CC TT CT TT TT CT TT CT
-rs7531583 A/G chr1 1696020 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7531583:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AG AA AG AG GG AG AA AA AA GG AG AG AG GG AG AG NN GG AA AG AG AG AG AG AA AG GG GG AA GG AG AG AG AG AG GG AG GG NN GG AG AG GG GG AG AG NN AA AG AG AG AA AG AG AG GG GG AG AG AG AG AA AG AG AG AG GG AG AG AG AA AA AG AA AG AG AA AG AA AG AA AA AG AA AG
-rs34238514 C/T chr1 1696595 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs34238514:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CT CT CC CC CT CC CC CC CC CC CT CC CC CC CC CC CC CC
-rs12041925 G/T chr1 1697600 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12041925:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT GT TT TT GT GT GG TT TT TT TT GT TT TT GT GT TT GT GT GT TT TT GT GT GT GT TT GT TT GT TT GT TT TT GT GT TT GT TT GG GT TT TT GT GT GT GT GT TT TT TT GT GT TT GT GT TT TT GT GT TT GT GT TT GT GT GT GT GT TT TT GT TT TT GT TT GT GT TT TT TT TT TT TT GT TT TT
-rs12044597 A/G chr1 1698661 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12044597:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AG AA AA AA AG AG AA AA AA AG AA AG AG AA AG AA AA AA AA AA AA GG AG AA AA AA AG AA AA AG AG AG AA AG GG AG AA AG AA AA AA AG AA AA AA AA AA AA AA AG GG AG AA AA AA AA AA AA AA AA AA AG AG AG AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AG
-rs867207 A/G chr1 1701274 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs867207:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AG AA AG AA AA AA AA AG AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AG AG AA AA AA AG AG AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AG GG AA AA AG AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs2272907 A/G chr1 1701558 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2272907:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs10907194 C/T chr1 1702090 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs10907194:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CC CT CT TT CC CC CC CC CC CC CC CT CT CC CC CT CT CC CC CT CT CT CT CC CT CC CT CC CC CC CC CT CT CC CT CC TT CT CC CC CC CT CT CT CT CC CC CC CT CT CC CT CT CC CC CT CT CC CC CC CC CT CT CT CC CT CC CC CT CC CC CT CC CT CT CC CC CC CC CC CC CT CC CC
-rs7534617 G/T chr1 1703729 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7534617:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT GT TT TT GT GT GG TT TT TT TT TT TT TT GT GT TT TT GT GT TT TT GT GT GT GT TT GT TT GT TT TT TT TT GT GT TT GT TT GG GT TT TT TT GT GT GT GT TT TT TT GT GT TT GT GT TT TT GT GT TT TT TT TT GT GT GT TT GT TT TT GT TT TT GT TT GT GT TT TT TT TT TT TT GT TT TT
-rs742359 A/C chr1 1704871 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs742359:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC AC CC CC AC AC AA CC CC CC CC CC CC CC AC AC CC CC AC AC CC CC AC AC AC AC CC AC CC AC CC CC CC CC AC AC CC AC CC AA AC CC CC CC AC AC AC AC CC CC CC AC AC CC AC AC CC CC AC AC CC CC CC CC AC AC AC CC AC CC CC AC CC CC AC CC AC AC CC CC CC CC CC CC AC CC CC
-rs6659884 G/T chr1 1707708 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6659884:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GT GG GG GG GG GG GT GG GG GG GG GG GG GG GG GG GG GG GG GG GT GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GT GT GG GG GG GG GG GG GG GG GG GG GG GG
-rs2272908 C/T chr1 1711339 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2272908:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CC CT CT CC CC CC CT CC CT CT CC CT CC CC CC CC CC CC TT CT CC CC CC CT CC CC CT CT CT CC CT TT CT CC CT CC CC CC CT CC CC CC CC CC CC CC CT TT CT CC CC CC CC CC CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CT
-rs3737626 A/C chr1 1712445 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3737626:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs3737628 C/T chr1 1712792 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3737628:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CC CT CT CC CC CC CT CC CT CT CC CT CC CC CC CC CC CC TT CT CC NN CC CT CC CC CT CT CT CC CT TT CT CC CT CC CC CC CT CC CC CC CC CC CC CC CT TT CT CC CC CC CC CC CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CT
-rs9660180 A/G chr1 1712891 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9660180:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG AG AG GG GG GG AG GG AG AG GG AG GG GG GG GG GG GG AA AG GG GG GG AG GG GG AG AG AG GG AG AA AG GG AG GG GG GG AG GG GG GG GG GG GG GG AG AA AG GG GG GG GG GG GG GG GG GG AG AG AG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG AG
-rs9970652 C/T chr1 1715486 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9970652:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CT CT CC CC CT CC CC CC CC CC CC CC CT CC CT CC CC CC CT CC CT CC CT CT CT CT CT CC CC CT CC CC CT CC CC CC CC CC CC CC
-rs12069909 A/G chr1 1717251 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12069909:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG AG GG AG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG AG GG GG AG GG AG GG GG GG GG GG GG AG GG GG AG GG AA AG GG GG GG GG AG AG GG GG GG GG AG AG GG GG AG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs10159187 A/G chr1 1721616 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs10159187:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AG AG AA AA AG AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs16825334 A/G chr1 1730263 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs16825334:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AG AA AA AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AG AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs12078713 C/T chr1 1731196 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12078713:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs16825336 A/G chr1 1735586 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs16825336:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG
-rs12742323 G/T chr1 1736554 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12742323:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GT GT GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GT GG GG GG GT GT GG GG GT GG GG GG GG GG GT GG GG GG GG GG GG GG
-rs2180311 C/T chr1 1738594 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2180311:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT CT TT TT TT CT CT TT TT TT CT TT CT CT TT CT TT TT TT TT TT TT CC CT TT TT TT CT TT TT CT CT CT TT CT CC CT TT CT TT TT TT CT TT TT TT TT TT TT TT CT CC CT TT TT TT TT TT TT TT TT TT CT CT CT TT TT TT TT TT TT TT TT CT TT CT TT TT TT TT CT
-rs4648726 C/T chr1 1742815 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648726:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CT CC TT CT TT CT CC CT CC TT CT CT CT TT CT CT TT CT CT TT CT CT CT TT CT TT TT TT CC TT CT CT CT CT TT TT TT TT TT TT CT CT TT TT CT TT TT CT TT TT CT CT CT CT CT TT TT TT CT TT CT CC CT TT CT TT TT TT TT TT CT TT TT CC TT CT CC TT CC CT CC CC CT CC CT
-rs12090110 A/G chr1 1747197 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12090110:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs9786963 C/T chr1 1748886 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9786963:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CT TT CC CT CC CT TT CT TT CC CT CT CT CC CT CT CC CC CT CC CT CT CT CC CT CC CC CC TT CC CT CT CT CT CC CC CC CC CC CC CT CT CC CC CT CC CC CT CC CC CT CT CT CT CT CC CC CC CT CC CT TT CT CC CT CC CC CC CC CC CT CC CC TT CC CT TT CC TT CT TT TT CT TT CT
-rs10907187 A/G chr1 1748914 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs10907187:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG AG AG AA GG GG GG GG GG GG GG AG AG GG GG AG AG GG GG AG AG AG AG GG AG GG AG GG GG GG GG AG AG GG AG GG AA AG GG GG GG AG AG AG AG GG GG GG AG AG GG AG AG GG GG AG AG GG GG GG GG AG AG AG AG AG GG GG AG GG GG AG GG AG AG GG GG GG GG GG GG AG GG GG
-rs9786942 A/G chr1 1749073 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9786942:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AG AA AA AA AG AG AA AA AA AG AA AG AG AA AG AA AA AA AA AA AA GG AG AA AA AA AG AA AA AG AG AG AA AG GG AG AA AG AA AA AA AG AA AA AA AA AA AA AA AG GG AG AA AA AA AA AA AA AA AA AA AG AG AG AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AG
-rs35517040 A/G chr1 1750999 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35517040:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs7553640 C/T chr1 1751874 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7553640:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CT TT CC CC CC CT TT CT TT CC CT CT CT CC CC CC CC CC CT CC CT CT CT CC CT CC CC CC TT CC CT CT CT CT CC CC CC CC CC CC CC CT CC CC CT CC CC CT CC CC CC CT CT CT CT CC CC CC CT CC CT TT CT CC CT CC CC CC CC CC CT CC CC TT CC CT TT CC TT CT TT TT CT TT CT
-rs11589067 A/G chr1 1753634 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11589067:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs6603797 C/T chr1 1755443 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603797:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CT TT CC CT CC CC TT CT TT CC CT CT CT CC CT CT CC CC CT CC CT CT CT CC CT CC CC CC TT CC CT CT CT CT CC CC CC CC CC CC CT CT CC CC CT CC CC CT CC CC CT CT CT CT CT CC CC CC CT CC CT TT CT CC CT CC CC CC CC CC CT CC CC TT CC CT TT CC TT CT TT TT CT TT CT
-rs12117139 C/T chr1 1763774 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12117139:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs11260622 A/G chr1 1765035 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260622:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs4648727 A/C chr1 1766129 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648727:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC AC CC CC AC AC AA CC CC CC CC AC CC CC AC AC CC AC AC AC AC AC AC AC AC AC CC AC CC AC CC AC CC CC AC AC AC AC AC AA AC CC CC AC AC AC AC AA AC CC CC AA AC CC AC AC CC CC AC AA CC AA AC CC AC AA AC AA AC AC AC AA AC AA AA CC AA AC CC AC CC CC CC CC AC CC AC
-rs12126768 G/T chr1 1767950 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12126768:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT GT TT TT TT TT TT TT TT TT GT GT TT TT GT TT TT TT TT TT TT TT GT TT GT TT TT TT GT TT GT TT GT GT GT GT GT TT TT GT TT TT GT TT TT TT TT TT TT TT
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-rs12403351 A/G chr1 1769090 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12403351:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs6681938 C/T chr1 1771080 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6681938:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT CT TT TT CT CT TT CT TT TT TT TT TT TT TT TT TT TT TT CT CT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
-rs12078176 G/T chr1 1777594 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12078176:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs4402075 C/T chr1 1781551 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4402075:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG NN GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs10907192 A/G chr1 1782971 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs10907192:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AG AA GG AG GG AG AA AG AA GG AG AG AG GG AG AG GG AG AG GG AG AG AG GG AG GG GG GG AA GG AG AG AG AG GG GG GG GG GG GG AG AG GG GG AG GG AG AG GG GG AG AG AG AG AG GG GG GG AG GG AG AA AG GG AG GG AG AG AG GG AG GG GG AA GG AG AG AG AA AA AA AA AG AA AG
-rs16824500 A/G chr1 1783072 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs16824500:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG GG AG GG GG GG GG AG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG AG AG AG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG AG AA GG GG AG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs7511905 A/C chr1 1783646 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7511905:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AC AC AA CC AC CC AC AA AC AA CC AC AC AC CC AC AC CC AC AC CC AC AC AC CC AC CC CC CC AA CC AC AC AC AC CC CC CC CC CC CC AC AC CC CC AC CC AC AC CC CC AC AC AC AC AC CC CC CC AC CC AC AA AC CC AC CC AC AC AC CC AC CC CC AA CC AC AC AC AA AA AA AA AC AA AC
-rs9660106 A/G chr1 1787807 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9660106:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AG AA AA AA AG AG AA AA AA AG AA AG AA AA AG AA AA AA AA AA AA GG AG AA AA AA AG AA AA AG AG AG AA AG GG AG AA AG AA AA AA AA AA AA AA AA AA AA AA AG GG AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG
-rs16824508 A/G chr1 1789051 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs16824508:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs4648592 A/G chr1 1790894 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648592:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG AG AG AA GG GG GG GG GG GG GG AG AG GG GG AG AG GG GG AG AG AG AG GG AG GG AG GG GG GG GG AG AG GG AG GG AA AG GG GG GG AG AG AG AG GG GG GG AG AG GG AG AG GG GG AG AG GG GG GG GG AG AG AG AG AG GG GG AG GG GG AG GG AG AG GG GG GG GG GG GG AG GG GG
-rs3855951 C/T chr1 1794162 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3855951:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CT CC TT CT TT CT CC CT CC TT CT CT CT TT CT CT TT CT CT TT CT CT CT TT CT TT TT TT CC TT CT CT CT CT TT TT TT TT TT TT CT CT TT TT CT TT CT CT TT TT CT CT CT CT CT TT TT TT CT TT CT CC CT TT CT TT CT CT CT TT CT TT TT CC TT CT CC CT CC CC CC CC CT CC CT
-rs12085733 C/T chr1 1795741 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12085733:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs11260624 C/T chr1 1799369 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11260624:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CC CT CT TT CC CC CC CC CC CC CC CT CT CC CC CT CT CC CC CT CT CT CT CC CT CC CT CC CC CC CC CT CT CC CT CC TT CT CC CC CC CT CT CT CT CC CC CC CT CT CC CT CT CC CC CT CT CC CC CC CC CT CT CT CT CT CC CC CT CC CC CT CC CT CT CC CC CC CC CC CC CT CC CC
-rs7525092 C/T chr1 1799950 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7525092:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CC CT CT TT CC CC CC CC CT CC CC CT CT CC CT CT CT CC CC CT CT CT CT CC CT CC CT CC CT CC CC CT CT CC CT CC TT CT CC CC CT CT CT CT CT CC CC CC CT CT CC CT CT CC CC CT CT CC CT CT CC CT CT CT CT CT CC CC CT CC CT TT CC CT CT CC CC CC CC CC CC CT CC CC
-rs6603803 A/G chr1 1802548 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603803:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AG AA AA AA AG AG AA AA AA AG AA AG AA AA AG AA AA AA AA AA AA GG AG AA AA AA AG AA AA AG AG AG AA AG GG AG AA AG AA AA AA AA AA AA AA AA AA AA AA AG GG AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG
-rs16824526 A/C chr1 1807989 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs16824526:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AC AA AA AA AA AA AA AA AA AA AA AC AA AC AA AA AA AA AC AC AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AA AA AA AC AA AA AA AA AA AA AA AA AA AC AA AA AA AA AC AA AA AA AC AC AA AA AC AA AA AA AA AA AC AA AA AA AA AA AA AA
-rs6603804 C/T chr1 1809238 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603804:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CT TT CC CT CC CT TT CT TT CC CT CT CT CC CT CT CC CT CT CC CT CT CT CC CT CC CC CC TT CC CT CT CT CT CC CC CC CC CC CC CT CT CC CC CT CC CT CT CC CC CT CT CT CT CT CC CC CC CT CC CT TT CT CC CT CC CT CT CT CC CT CC CC TT CC CT TT CT TT TT TT TT CT TT CT
-rs35371819 G/T chr1 1809844 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35371819:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
-rs6603805 A/G chr1 1811485 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603805:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG GG GG AG AG AA GG GG GG GG AG GG GG AG AG GG AG AG AG GG GG AG AG AG AG GG AG GG AG GG AG GG GG AG AG GG AG GG AA AG GG GG AG AG AG AG AG GG GG GG AG AG GG AG AG GG GG AG AG GG AG AG GG AG AG AG AG AG GG GG AG GG AG AA GG AG AG GG GG GG GG GG GG AG GG GG
-rs6688000 A/G chr1 1813782 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6688000:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AG AA GG AG GG AG AA AG AA GG AG AG GG GG AG AG GG AG AG GG AG AG AG GG AG GG GG GG AA GG AG AG AG AG GG GG GG GG GG GG AG AG GG GG AG GG AG AG GG GG AG AG AG AG AG GG GG GG GG GG GG AA AG GG AG GG AG AG AG GG AG GG GG AG GG AG AA AG AA AA AA AA AG AA AG
-rs12093735 C/T chr1 1817072 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12093735:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CT CC CT CC CT CC CC CC CC CC CC CT CC CT CC CC CC CC CC CC CT CC CC CT CC CC CC CC CC CC CC CC CC CC CC CT CC CT CT CC CC CC CC CT CC CC CC CC CT CC CC CC CC CT CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs745910 C/T chr1 1819342 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs745910:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT CT TT TT TT TT TT TT TT TT TT CT TT TT TT TT CT TT TT TT CT CT TT TT CT TT TT TT TT TT CT TT TT TT TT TT TT CT
-rs4648732 C/T chr1 1827738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648732:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CT CC CC CT CT CC CC CT CT CC CT CC TT CT CC CC CT CT CC CC CC CT CT TT CC CT CC CT TT CC CT CT TT CT CT CC CT CT CC CC CC CC CT TT CT TT CT CC CT TT CT CT TT CT CC CC CT TT TT CC CC CC CT CT CT CT CT CC CC CT CC CC CT CT CT CT CT CC CC CC CT CT TT CT CT
-rs28625223 C/T chr1 1828033 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28625223:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT CT TT TT TT TT TT TT TT TT CT TT TT TT TT CT TT TT TT CT TT TT TT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT TT TT CT TT TT TT TT CC CT TT TT TT CT CT TT TT TT CT CT CT CT TT CT TT TT TT TT TT TT TT TT TT TT
-rs2377037 A/C chr1 1828376 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2377037:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC AC CC CC CC CC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC AC CC CC AC CC CC CC CC CC CC CC CC CC CC AC AC CC CC CC CC AC CC CC CC CC NN CC AC CC CC CC CC AC AC CC CC CC CC CC CC CC CC CC
-rs28659907 G/T chr1 1831675 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28659907:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT GT TT GT TT TT TT TT TT TT GT TT GT TT TT TT TT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT GT NN TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT
-rs2474460 C/T chr1 1833906 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2474460:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CC CT CT CC CC CC CT CC CT CC CC CT CC CC CC CC CC CC CT CT CC CC CC CT CC CC CT CT CT CC CT TT CT CC CT CC CC CC CC CC CC CC CC CC CC CC CT TT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC
-rs2748988 A/G chr1 1836217 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2748988:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG AG AG GG GG GG AG GG AG GG GG AG GG GG GG GG GG GG AA AG GG GG GG AG GG GG AG AG AG GG AG AA AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG AA AG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG
-rs2748987 A/G chr1 1836442 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2748987:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG AG GG GG GG GG AA GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG AG GG GG GG AG GG GG GG AG AG AG AA AG GG GG GG GG GG
-rs2247560 A/G chr1 1836625 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2247560:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG AG AG GG GG GG AG GG AG GG GG AG GG GG GG GG GG GG AA AG GG GG GG AG GG GG AG AG AG GG AG AA AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG AA AG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG
-rs28710181 C/T chr1 1837391 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28710181:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CC CT CC CT CT CC CT CC CT CC CC CC CT CC CC CT CT CC CC CT CC CT CC CC CC CT CT CC CT CC CT CT CC CC CC CT CC CT CC CC CC CT CC CC CT CT CC CT TT TT CC CT CT CT CT CC CC CC CT CT CC CT TT CT CC CC CC CT CT CT CC CT CT TT CT CC CC CT CT CC CT CT CT CT CT CC
-rs2748986 G/T chr1 1837716 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2748986:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT GG GT GG GT GT GG TT GG GT GG GT GT GT GG GG TT GT GT GG GT GT GT GG GG GG GT GT TT TT GG GT GT GT GG GG TT GT TT GG GT TT TT GG GT GT GT GG GT TT TT GG GT GT GT GT GT TT GT GT GT GG GT TT GT GG GG GG TT GT TT GG GT GT TT GT GG GG GT GT GG GT GT GT GT GT GT
-rs941532 A/G chr1 1838594 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs941532:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs2490548 A/G chr1 1841994 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2490548:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AG AA AA AA AG AG AA AA AA AG AA AG AA AA AG AA AA AA AA AA AA GG AG AA AA AA AG AA AA AG AG AG AA AG GG AG AA AG AA AA AA AA AA AA AA AA AA AA AA AG GG AG AA AA AA AA AA AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG
-rs28508199 A/G chr1 1842344 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28508199:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG AG GG GG GG AG AA GG AG AA AA GG AG GG AG AG AG GG AG AA GG GG AG GG GG GG AA AG AA AG AG AA AG GG AG AG AG GG AG AA AG AG AG GG GG GG GG GG GG GG GG GG AG GG AA AA AG GG AG GG GG GG GG AG GG GG GG AG AG GG GG AG GG AG GG AG AG AG AA AG AG GG AG AG AG
-rs2803349 C/T chr1 1842632 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2803349:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CC CC CT CT CC CC CC CT CC CT CC CC CT CC CC CC CC CC CC TT CT CC CC CC CT CC CC CT CT CT CC CT TT CT CC CT CC CC CC CC CC CC CT CC CC CC CC CT TT CT CC CC CC CC CC CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT
-rs1884454 G/T chr1 1843148 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1884454:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG TT GT TT GT GG GT GT TT GG GT GT GG GT GT TT GG GT GT TT GG GG GT TT TT TT GT GT GG GG GG GT GG GG GT TT GG GT GG TT GT GG GG GT GT GT GT TT GT GG GG TT GT GG GG GT GT GG GT GT GG TT GT GG GT GT TT TT GG GG GG TT GT GG GG GG TT TT GT GG TT GT GG GG GG GG GT
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-rs28637822 C/T chr1 1851885 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28637822:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC NN CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC NN CC CC CC NN
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-rs2803329 A/G chr1 1864441 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2803329:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG AG AG GG GG GG GG AA GG GG GG GG GG GG GG AG GG AG GG AG AG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG AA AG GG GG AG GG GG GG AG AG GG AA AG GG GG GG GG GG
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-rs35375532 C/T chr1 1867212 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs35375532:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CT CT CC CC CC CC TT CC CC CC CC CC CC CC CT CC CT CC CT CT CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC TT CT CC CC CT CC CC CC CT CT CC TT CT CC CC CC CC CC
-rs3820011 A/C chr1 1878053 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3820011:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AC AC CC CC CC NN CC AC CC CC CC CC CC CC AC AC CC CC AC AC CC CC CC AA AC CC CC CC CC CC CC CC CC CC AC AC CC CC CC AC CC AC AC CC AA AC AC AC CC CC CC AC AC AC CC CC AC AC AC AC CC CC CC CC AC AA AC CC CC CC CC AC CC CC CC CC AC AC CC CC CC CC CC CC CC CC CC
-rs2803291 C/T chr1 1882185 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2803291:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CT CC CT CC CC CC CT CC CT CC CT CC CT CC CT CC CC CC CT CC CC CC CC CC CT CC TT CC CT CT CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CC CC CT CC CC CC CT CC CT CC CC CC CC CC CC CC CC CT CC CC CT CT CC CT CC CC CT CC CT CT CT CC CT TT CC
-rs16824588 C/T chr1 1890092 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs16824588:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT TT TT TT CT TT CT TT CT CT CT CC CT CT CT CC CC CC CT CT TT CT CC CT CT TT TT CT TT CC CT CT CT CC TT CT CC TT CC CT CT CC CT CC CT CT TT TT TT TT CT CC CC CT CT CC CT CC CT CT TT TT TT CT CC CT TT CT CT TT TT TT CT TT CT TT TT TT CT TT TT CT CT CT CT CT
-rs4648745 C/T chr1 1904125 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648745:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CT CT TT CT TT CC CT TT TT TT TT CT TT TT TT TT TT TT CC CT CT CC CC CT TT TT TT TT TT CT CT TT TT TT TT TT CT CT TT CT CC TT CC CT CT TT CT TT TT TT TT CC TT TT CT CT CT CT CC TT TT TT CT CC CT CC CT TT CT CT CT TT TT CT CT CT TT CC CT CT TT CT TT TT CT
-rs3795283 G/T chr1 1906447 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3795283:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GT GT GG GT GG TT GT GG GG GG GG GT GG GG GG GG GG GG TT GT GT TT TT GG GG GG GG GG GG GT GT GG GG GG GG GG GT GT GG GT TT GG TT GT GT GG GT GG GG GG GG TT GG GG GT GT GT GT TT GG GG GG GT TT GT TT GT GG GT GT GT GG GG GT GT GT GG TT GT GT GG GT GG GG GT
-rs6661597 C/T chr1 1915947 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6661597:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CC CT CC CT CT CC CC CC CT CC CT CC CT CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC CT CT CT CC CT CC CC CC CT CC CC CT CC CC CC CC CC CC CC CC CC CT TT CT CC CC CC CT CC CT CC CC CC CC CT CT CC CC CC CC CT CT CC CT CC CC CC CC CC CC CC
-rs6605081 C/T chr1 1920614 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6605081:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CC CC CT CT CT CT CC CT CT CT CC CT TT TT CC CT CT CT CT CT TT TT CT TT TT TT CT CT CT CC CC CT TT CC CT CT CT CT CT CT TT CT CT CT CT CT CT TT TT CT CT CT CT CT CT CT CC CT TT CT CT CT TT CC CT TT CT CT CC CT TT TT TT TT CT CC CT CC CT CT CT CC TT TT CT
-rs6656398 A/G chr1 1931789 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6656398:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AG GG AG AG AG GG AG AG AA AA AA AG AA AG AG GG AA AA AG AG AG AA AA AA AA AA GG GG AA AA AA AA AG AG AG AA AG AG AA AG AA GG AG AG GG AA AA AA AA AG AG AG AA AA AA AA AA AG AG AA AA AG AA AG AG AA AA AG GG AA AG AA AA AG AA AG AA AA AG AA AA AG AA AG AG
-rs13303016 A/G chr1 1936451 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13303016:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AG AA AG GG AA AA AA AA AA AG AA AG AA AG AA AA AA AA AG AA AA AA AA AA AA AG AA AA AA AA AG AA AG AA AG AG AA AA AG AG AG AG AG AA AA AA AA AG AG AG AA AA AA AA AA AG GG AA AA AG AA AG AG AA AA AA AG AA AG AA AA AG AA AA AA AA AA AA AA AG AA AG AA
-rs13303344 A/C chr1 1938260 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs13303344:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AC AA AC AC AC AC CC AA AC AA AA AA AC AA AC AC CC AA AC AC AC AC AA AA AA AA AA CC CC AA AC AC AA AC AA AC AA AC AC AA AC AC AC AC AC AC AA AA AA AA AC AC AC AA AA AA AA AA AC CC AA AA AC AA AC AC AA AA AC CC AA AC AA AA AC AA AA AA AA AA AA AA AC AA AC AC
-rs4481796 C/T chr1 1938665 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4481796:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CT CC CT TT CC CC CC CC CC CT CC CT CC CT CC CC CC CC CT CC CC CC CC CC CC CT CC CC CC CC CT CC CT CC CT CT CC CC CT CT CT CT CT CC CC CC CC CT CT CT CC CC CC CC CC CT TT CC CC CT CC CT CT CC CC CC CT CC CT CC CC CT CC CC CC CC CC CC CC CT CC CT CC
-rs28603108 A/G chr1 1940481 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28603108:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AG AA AG GG AA AA AA AA AA AG AA AG AA AG AA AA AA AA AG AA AA AA AA AA AA AG AA AG AG AA AG AA AG AA AG AG AA AA AG AG AG AG AG AA AA AA AA AG NN AG AA AA AA AA AA AG GG AA AA AG AA AG AG AA AA AA AG AA AG AA AA AG AA AA AA AA AA AA AA AG AA AG AA
-rs3121819 A/G chr1 1941687 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3121819:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG AG GG AG AG GG GG GG GG GG AG GG AG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG AG GG GG GG GG GG AG GG GG GG AG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG AG GG AG GG
-rs3128318 A/C chr1 1942642 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128318:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AC AA AC AC AA AA AA AA AA AC AA AC AA AA AA AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AC AC AA AA AA AA AA AA AA AA AC AA AA AA AA AA AC AC AA AA AC AA AA AA AA AA AA AC AA AC AA AA AA AA AA AA AA AA AA AA AC AA AC AA
-rs28669111 C/T chr1 1943926 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs28669111:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs3128322 A/G chr1 1944296 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128322:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AA AG AG AG AG GG AA AA AA AA AA AG AA AG AG GG AA AA AA AA AG AA AA AA AA AA AA AG AA AG AG AA AA AA AG AA AG AG AA AA AG AG AG AG AG AA AA AA AA AG AG AG AA AA AA AA AA AG GG AA AA AG AA AG AG AA AA AA AG AA AG AA AA AG AA AA AA AA AA AA AA AG AA AG AA
-rs3128323 A/G chr1 1944940 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128323:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AG AA AG AG AA AG AA AA AA AG AA AG AA AA AA AA AA AA AG AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AG AA AA AA AA AA AG AA AA AA AG AA AA AA AA AA AA AG AA AG AA AA AA AA AA AA AA AA AA AA AG AA AG AA
-rs17715203 A/G chr1 1953275 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs17715203:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG GG GG AG GG AG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG AG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG AG GG AG AG
-rs7554461 A/G chr1 1955656 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs7554461:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs9442614 A/G chr1 1958691 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9442614:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG GG GG AG GG AG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG AG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG
-rs3121822 C/T chr1 1962322 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3121822:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT TT TT CT TT TT CT TT CT TT TT TT TT CT TT TT TT CT CC TT TT CT TT TT TT TT TT TT TT TT CT CT TT TT CT CT TT CT TT TT TT TT CT TT TT TT TT TT TT TT TT TT TT CT CC TT TT TT TT CC TT TT TT TT TT TT TT TT TT TT TT TT CT CC CT TT TT TT TT CT CT CT CC CT CT TT
-rs3128317 A/C chr1 1969584 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128317:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC AC AC CC CC CC CC CC CC CC CC CC CC CC CC CC CC AC CC AC AC CC CC CC AC CC CC AC AC CC CC CC AC CC AC CC CC CC CC CC AC CC CC CC CC AC AA CC CC CC CC CC CC CC AC CC CC CC CC AC CC CC AC CC CC CC CC CC CC AC CC CC CC CC CC CC CC CC CC CC CC
-rs3795277 A/C chr1 1970978 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3795277:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AC AC AA AA AA AA AA AA AC AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AC AC AA AA AA
-rs6692648 C/T chr1 1972257 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6692648:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT CT CT CT CT CC TT TT CC TT TT TT TT CT TT CT CT TT CT TT TT TT TT CT TT TT TT TT TT TT CC CT TT CT TT CT CT CT TT TT TT TT TT TT TT TT TT CT TT TT CT TT CT TT CT TT TT TT TT TT CT TT TT TT TT TT TT CT TT TT TT TT TT TT TT TT CT CT TT CT TT CT CT CT CT CT
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-rs884080 A/G chr1 2016609 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs884080:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG AG AG GG AG GG AG AG AG GG AA AG GG AG AG AA AG AG GG AG AG GG AG AG AG AG GG GG GG GG GG GG GG GG GG AA AG AA GG GG AG GG GG AG GG GG AG AG GG GG AG AA AG GG GG GG AG AG GG GG AG GG GG GG GG GG GG AG AG GG GG GG AG GG GG GG GG AG AG GG GG AG GG AG AG AG
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-rs908742 A/G chr1 2023116 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs908742:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG AG AG GG GG GG GG GG AA AG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG AG GG GG GG GG AG AG GG GG GG GG AG AG GG AG GG AG GG GG GG GG GG
-rs10910029 A/G chr1 2025239 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs10910029:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AG GG AA AG AA AG AG AA AA GG AG AA AG AG AG AA AG AA AG AG AG GG GG AA AG AG AA AA AG AA AA AG AG AA AG AG AG AA AA AG AA AG AG AA AG AG AA AG AG AA AG AA AA AA AA AG AG AA AG AG AG AG GG AG AA AA AG AG AA AA AA AG AA AG AA AA AG AG AG AA AG AG AA AG AG
-rs10910030 C/T chr1 2025544 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs10910030:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CT TT CC TT CT CT CT CT CC TT CT CC TT CT CT CC CT CC TT CT TT TT TT CT CT TT CC CC CT CC CC CT TT CC CT CT CT CC CC CT CC CT CT CC CT TT CT CT CT CC CT CC CC CT CC CT CT CT CT CT CT CT TT CT CC CC CT CT CC CC CT CT CC CT CC CC CT CT CT CC CT TT CC CT CT
-rs10752741 A/G chr1 2025659 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs10752741:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG AG AA GG AA AG AG AG AG GG AA AG GG AA AG AG GG AG GG AA AG AA AA AA AG AG AA GG GG AG GG GG AG AA GG AG AG AG GG GG AG GG AG AG GG AG AA AG AG AG GG AG GG GG AG GG AG AG AG AG AG AG AG AA AG GG GG AG AG GG GG AG AG GG AG GG GG AG AG AG GG AG AA GG AG AG
-rs10797413 A/G chr1 2026123 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs10797413:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG AG AA GG AA AG AG AG AG GG AA AG GG AA AG AG GG AG GG AA AG AA AA AA AG AG AA GG GG AG GG GG AG AA GG AG AG AG GG GG AG GG AG AG GG AG AA AG AG AG GG AG GG GG AG GG AG AG AG AG AG AG AG AA AG GG GG AG AG GG GG AG AG GG AG GG GG AG AG AG GG AG AA GG AG AG
-rs12410859 C/T chr1 2028592 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12410859:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CT CC CC CC CC CT CC CC CC CC CC CC CC CT CC CC CC CC CC CC TT CT CC CC CC CT CC CT CC CC CC CC CT CT CC CC CC CT CC CC CC CC CC CT CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CT CT CC CT CC CT CC CC CC CC CC
-rs1878752 A/G chr1 2029579 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1878752:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG AG AA GG AA AG AG AG AG GG AA AG AG AA AG AG GG AG GG AA AA AA AA AA AG AG AA AA AG AG AA AG AA AA AG AA AG AA GG AG AG NN AG AG AG AG AA AG AG AG AA AA GG GG AA GG AG AA AA AG AG AG AA AA AG GG GG AG AA AA AG AG AG GG AG AG AG AA AA AG AG AG AA GG AG AA
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-rs4648807 C/T chr1 2030758 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648807:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CT CC TT CT TT CT TT TT TT CC CT TT CT CT CT TT CT TT CT CT CT CC CC TT CT CT TT TT CT TT TT CT CT TT CT CT CT TT TT CT TT CT CT TT CT CT TT CT CT TT TT TT TT TT TT CT CT TT CT CT CT CC CC CT TT TT CT CT TT TT CT CT TT CT TT TT CT CT CT TT CT CT TT CT CT
-rs4648808 C/T chr1 2030796 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs4648808:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT CT CT CC TT CC CT CT CT CT TT CC CT CT CC CT CT TT CT TT CC CC CC CC CC CT CT CC CC CT CT TT TT CC CC CT CC CT CC TT CT CT TT CT CT CT CT CC CT CT CT CT CT TT TT CT TT CT CC CC CT CT CT CC CC CT TT TT CT CT CT CT CT CT TT CT CT CT CT CC CT CT CT CC TT CT CC
-rs11584491 A/G chr1 2032403 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs11584491:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AG AG GG AA AG AA AG AA AA AA GG AG AA AG AG AG AA AG AA AG AG AG GG GG AA AG AG AA AA AG AA AA AG AG AA GG AG GG AA AA AG AA AG AG AA AG AG AA AG AG AG AA AA AA AA AA AG AG AA AG AG AG GG GG AG AA AA AG AG AA AA AA AG AA AG AA AA AG AG AG AA AG AG AA AG GG
-rs6603813 G/T chr1 2032940 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs6603813:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT GT GT TT GT GT TT TT TT GT GT TT TT TT TT TT GT GT GT TT TT GT TT GT GG GT TT TT TT GT GT GT TT TT TT TT GT TT TT TT TT GT TT GT GT TT TT TT GT TT TT GT TT TT GT GG TT TT TT TT TT TT TT TT TT TT GT GT GT TT TT TT GT GT TT GT TT GT TT GT TT TT TT
-rs3128337 A/G chr1 2035742 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128337:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG GG GG GG GG GG AG AG AG GG GG GG AG GG GG GG GG GG AG GG AG GG GG GG AG GG AG AA AG GG AA AG AG GG AG AG GG AG AG AA AG AG GG AG AG GG GG GG GG GG AG GG GG GG AG AG AG AG AG GG GG AG GG GG GG GG AG GG AG AA AA AG GG GG GG AA AG GG AG GG AG GG AG GG GG AG
-rs3107145 A/G chr1 2037407 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3107145:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AG AG AG AA AA AA AG AA AA AA AA AA AG AA AG AA AA AA AG AA AG GG AG AA AA AA AG AA AG AA AA AA AG GG AG AG AA AG AG AA AA AA AA AA AA AA AA AA AA AG AG AG AG AA AA AG AA AA AA AA AG AA AA AG GG AG AA AA AA GG AG AA AG AA AG AA AG AA AA AA
-rs3107146 C/T chr1 2037444 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3107146:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CC CC CT CT CT CT CC CT CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CT CC CC CC CC CT CC CC CC CT CT CC CC CC CT CC CC CC CC CC CC CT CC CC CC
-rs3107147 A/G chr1 2038589 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3107147:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AA AA AA AA AG AG AG AG AG AA AA AA AG AG AA AA AA AA AG AA AG AA AA AA AG AA AG GG AG AA AA AA AG AG NN AA AA AA AG GG AG AG AA AG AG AA AG AG AA AA AA AG AA AA AG AG AG AG GG AA AA AG AA AA AA AA AG AA AA AG GG AG AA AA AA GG AG AA AG AA AG AA AG AA AA AA
-rs3107151 G/T chr1 2041373 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3107151:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GT GG GG GG GG GT GT GT GT GT GG GG GG GT GT GG GG GG NN GT GG GT GG GG GG GT GG GT TT GT GG GG GG GT GT GT GG GG NN GT TT GT GT GG GT GT GG GT GT GG GG GG GT GG GG GT GT GT GT TT GG GG GT GG GG GG GG GT GG GG GT TT GT GG GG GG TT GT GG GT GG GT GG GT GG GG GG
-rs3107153 C/T chr1 2046595 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3107153:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CT CT TT CC TT CT TT CT CT CC TT CT CT TT CT CT CC CT CT CT TT CT TT TT CC CT CT TT TT CT TT CT TT TT CT TT CT TT CT TT TT CT CT TT CT CT TT CT CT CT TT TT CC CC TT CT TT TT TT CT CT TT TT TT CT CC CT CT TT TT TT CT CT CC CT TT CT TT TT CT CT CT TT CC CT TT
-rs3128291 A/G chr1 2047883 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128291:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG AG AG AG GG AG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG AG GG GG GG GG AG GG GG GG AG AG GG GG GG AG GG GG GG GG GG GG AG GG GG GG
-rs3107157 C/T chr1 2051829 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3107157:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT CC CC CC CC CC CC CT CT CT CC CC CC CT CC CC CC CC CC CT CC CT CC CC CC CT CC CT TT CT CC CC CC CT CC CT CC CC CC CT TT CT CT CC CT CT CC CT CT CC CC CC CT CC CC CT CT CT TT TT CC CC CT CC CC CC CC CT CC CC CT TT CT CC CC CC TT CT CC CT CC CT CC CT CC CC CC
-rs3128296 G/T chr1 2058766 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128296:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GT TT TT TT TT TT TT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT GT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT GT TT TT TT TT GT GT GT TT TT GT TT TT TT GT GT TT TT TT GT TT TT TT TT TT TT TT TT TT TT
-rs425277 C/T chr1 2059032 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs425277:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CC CT CC CC CC CC CT CC CC CC CC CC CC CC CT CC CC CC CC CC CC TT CT CC CC CC CT CC CT CC CC CC CC CT CC CC CC CC CT CC CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CT CT CC CT CC CT CC CC CC CC CC
-rs16824860 G/T chr1 2059677 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs16824860:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs3128297 C/T chr1 2059960 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128297:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CC CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC CT CC CT CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CC CC CC CC CT CC CC TT CC CC CT CC CC CC CT CC CC CC CC CT CC CC CC CT CT CC CC CC CT CC CC CC CC CC CC CT CC CC CC
-rs424079 A/C chr1 2061200 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs424079:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC AA AA AA CC AC CC AC AC AC CC AA AC CC AC AC AA AA AA CC AA AC AA AA AA AC AA AC CC AC AC CC CC AC AC AC AC AC AC AC CC AA AA AA AA AC AA AC AC AA AC AA AC AA AC CC AA AA CC CC AA AA AC AA AA AA AC CC AA AC CC CC AC AA AA AA CC AC AA AC AA AC AA AC AA AA AA
-rs12026349 G/T chr1 2063964 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs12026349:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GT GG GT GG GG GG GG GT GT GT GG GG GG GG GT GG GG GG GG GT GG GG GG GG GG TT GT GT GG GG GG GG GG GG GT GG GG GG GG GT GT GG GG GG GG GG GG GG GT GG GG GG GT GG GG GT GG GG GT GG GG GG GT GG GG GG GG GT GT GG GG GT GT GG GG GG GT GG GG GG GG GG GG GT GG GG GG
-rs451061 C/G chr1 2064928 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs451061:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC GG CG GG CC CG CC CG CC CG CC GG CG CC CG NN GG GG GG CC GG CG GG GG GG CC CG CG CC CG CG CC CC CG CG CG NN NN CG CG CC GG GG GG GG CG GG CG CC GG CG GG CG CG CG CC GG GG CC CC GG GG CG GG GG GG CG CC CG CG CC CC CG GG GG GG CC CG GG CG GG CG GG CG GG GG GG
-rs427811 G/T chr1 2065420 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs427811:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT TT TT TT TT TT TT GT TT TT TT TT GT TT TT TT TT TT TT TT GT TT TT TT TT TT TT GG GT TT TT TT GT TT GT TT TT TT TT GT TT TT TT TT GT TT TT TT TT TT TT TT GT TT TT TT TT GT GT TT TT TT TT TT TT TT TT TT TT GT GT TT TT TT TT GT GT TT GT TT GT TT TT TT TT TT
-rs377283 C/T chr1 2065430 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs377283:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CT TT CT TT TT TT TT CT CC CT TT TT TT CT CT TT TT TT TT CT TT CT TT TT TT CC CT CT CC CT TT TT TT CT CT CT TT TT TT CT CC TT TT TT TT CT TT TT CT TT TT TT CT CT TT CC TT TT CC CT TT TT CT TT TT TT TT CT CT TT CT CC CT TT TT TT CC CT TT CT TT CT TT CT TT TT TT
-rs385039 A/G chr1 2067269 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs385039:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AG AA AA AA AA AG AA AA AA AA AA AA AA AG AA AA AA AA AA AA GG AG AA AA AA AG AA AG AA AA AA AA AG AA AA AA AA AG AA AA AA AA AA AA AA AG AA AA AA AA AG AG AA AA AA AA AA AA AA AA AA AA AG AG AA AA AA AA AG AG AA AG AA AG AA AA AA AA AA
-rs2257684 A/G chr1 2067732 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2257684:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AA AG AA AA AA AA AG GG AG AA AA AA AG AG AA AA AA AA AG AA AG AA AA AA GG AG AG GG AG AA AA AA AG AG AG AA AA AA AG GG AA AA AA AA AG AA AA AG AA AA AA AG AG AA GG AA AA GG AG AA AA AG AA AA AA AA AG AG AA AG GG AG AA AA AA GG AG AA AG AA AG AA AG AA AA AA
-rs262672 G/T chr1 2070673 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262672:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GT GG GG GG GG GT GG GG GG GG GG GG GG GT GG GG GG GG GG GG TT GT GG GG GG GT GG GT GG GG GG GG GT GG GG GG GG GT GG GG GG GG GG GG GG GT GG GG GG GG GT GT GG GG GG GG GG GG GG GG GG GG GT GT GG GG GG GG GT GT GG GT GG GT GG GG GG GG GG
-rs3107126 A/C chr1 2071502 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3107126:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA CC AC CC AA AC AA AC AC AC AA CC AC AC AC AC CC CC CC AA CC CC CC CC CC AA AC AC CC CC AC AA AA CC AC CC AC AC AC AC AC CC CC CC CC CC CC AC AA CC AC CC AC CC AC AC CC CC AC AC CC CC AC CC CC CC AC AA AC AC AC AC AC CC CC CC AC CC CC CC CC CC CC AC CC CC CC
-rs262669 A/G chr1 2072349 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262669:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG GG AG GG GG GG GG AG AA AG GG GG GG AG AG GG GG GG GG AG GG AG GG GG GG AA AG AG AA AG GG GG GG AG AG AG GG GG GG AG AA GG GG GG GG AG GG GG AG GG GG GG AG AG GG AA GG GG AA AG GG GG AG GG GG GG GG AG AG GG AG AA AG GG GG GG AA AG GG AG GG AG GG AG GG GG GG
-rs9442619 C/T chr1 2072365 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs9442619:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CT CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CC CT CC CC CC CC CC TT CT CT CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CT CC CC CC CT CC CC CT CC CC CT CC CC CC CT CC CC CC CC CT CT CC CC CT CT CC CC CC CT CC CC CC CC CC CC CT CC CC CC
-rs2257182 C/T chr1 2072426 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2257182:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CT TT CC CT CC CT CC CC CC TT CT CC CT CT CT CC CT CC TT CT TT TT TT CC CT CT CC CC CT CC CC CT CT CC CT CT CT CC CC TT CT CT TT CC CT CT CC CT CT CC CC CC CC CC CT TT CC CC CT CT CT CT TT CT CC CC CT CT CC CC CT CT CC CT CC CC CC CT CT CC CT CT CC CT CT
-rs262663 C/T chr1 2074458 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262663:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC TT CT TT CC CT CC CT CC CT CC TT CT CC CT CT TT TT TT CC TT CT TT TT TT CC CT CT CC CT CT CC CC CT CT CT CT CT CT CT CC TT TT TT TT CT TT CT CC TT CT TT CT CT CT CC TT TT CC CC TT TT CT TT TT TT CT CC CT CT CC CC CT TT TT TT CC CT TT CT TT CT TT CT TT TT TT
-rs262662 A/G chr1 2074893 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262662:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AA AG AA AA AA AA AG GG AG AA AA AA AG AG AA AA AA AA AG AA AG AA AA AA GG AG AG GG AG AA AA AA AG AG AG AA AA AA AG GG AA AA AA AA AG AA AA AG AA AA AA AG AG AA GG AA AA GG AG AA AA AG AA AA AA AA AG AG AA AG GG AG AA AA AA GG AG AA AG AA AG AA AG AA AA AA
-rs2459984 A/G chr1 2076172 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2459984:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG AG AG AA GG AG GG AG GG GG GG AA AG GG AG AG AG GG AG GG AA AG AA AA AA GG AG AG GG GG AG GG GG AG AG GG AG AG AG GG GG AA AG AG AA GG AG AG GG AG AG GG GG GG GG GG AG AA GG GG AG AG AG AA AA AG GG GG AG AG GG GG AG AG GG AG GG GG AG AG AG GG AG AG GG AG AG
-rs3123592 C/T chr1 2077417 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3123592:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ TT TT CT TT TT TT TT CT CT CT TT TT TT TT TT TT TT TT TT CT TT TT TT TT TT CC CT CT TT TT TT TT TT TT TT TT TT TT TT CT CT TT TT TT TT TT TT TT CT TT TT TT CT TT TT CT TT TT CT TT TT TT CT TT TT TT TT CT CT TT TT CT CT TT TT TT CT TT TT TT TT TT TT CT TT TT TT
-rs262657 A/G chr1 2078437 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262657:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AA AG GG GG GG AG GG AG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG AG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG AG AG GG AG GG AG GG GG GG GG GG
-rs262656 A/C chr1 2078614 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262656:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AC AA AA AA AA AC AA AA AA AA AA AA AA AC AA AA AA AA AA AA CC AC AA AA AA AC AA AC AA AA AA AA AC AA AA AA AA AC AA AA AA AA AA AA AA AC AA AC AA AA AC AC AA AA AA AA AA AA AA AA AA AA AC AC AA AA AA AA AC AC AA AC AA AC AA AA AA AA AA
-rs262654 A/G chr1 2079386 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262654:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG AA AG GG GG GG AG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG
-rs262653 G/T chr1 2079955 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262653:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG TT GT TT GG GT GG GT GG GT GG TT GT GG GT GT TT TT TT GG TT GT TT TT TT GG GT GT GG GT GT GG GG GT GT NN GT GT GT GT GG TT TT TT TT GT TT GT GG TT GT TT GT GT GT GG TT TT GG GG TT TT GT TT TT TT GT GG GT GT GG GG GT TT TT TT GG GT TT GT TT GT TT GT TT TT TT
-rs262651 A/G chr1 2081257 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262651:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AG AA AA AA AA AG AA AA AA AA AA AA AA AG AA AA AA AA AA AA GG AG AA AA AA AG AA AG AA AA AA AA AG AA AA AA AA AG AA AA AA AA AA AA AA AG AA AA AA AA AG AG AA AA AA AA AA AA AA AA AA AA AG AG AA AA AA AA AG AG AA AG AA AG AA AA AA AA AA
-rs3052 C/T chr1 2086498 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3052:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CC CT CC CC CC CC CT CT CT CC CC CC CC CC CC CC CC CC CC CC CC CC CC CC TT CT CT CC CC CC CC CC CC CC CC CC CC CC CT CT CC CC CC CC CC CC CC CT CC CC CC CC CC CC CT CC CC CT CC CC CC CT CC CC CC CC CT CT CC CC CT CT CC CC CC CT CC CC CC CC CC CC CT CC CC CC
-rs262641 A/G chr1 2094841 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262641:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AG AA AA AA GG AG GG AA AG AA AG AA AA GG AG AG AA AA AA AG AA AG AA AA AA AA AA AA GG AG AA GG AG AG AG AG AG AG AG AA AG AA AA AA AA AG AA AG AG AA AG AA AA AG AA AA AA AA AG GG AA AA AA AA AA AA AG AG AA AG GG AG AA AA AA AA AG AG AA AG AA AG AA AA AA AA AA
-rs3128309 A/G chr1 2095738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs3128309:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG AG GG GG GG AG GG GG GG GG AG GG GG GG AG AG GG GG GG AG GG GG GG GG GG GG GG GG GG GG
-rs2292857 A/G chr1 2096298 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2292857:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG
-rs1467727 G/T chr1 2099133 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs1467727:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA NN AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA AA
-rs2460001 C/T chr1 2100890 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs2460001:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC CT CT TT CC CT CC CT CC CC CC TT CT CC CT CT CT CC CT CC TT CT TT TT TT CC CT CT CC CC CT CC CC CT CT CC CT CT CT CC CC TT CT CT TT CC CT CT CC CT CT CC CC CC CC CC CT TT CC CC CT CT CT TT TT CT CC CC CT CT CC CC CT CT CC CT CC CC CT CT CT CC CT CT CC CT CT
-rs262689 A/G chr1 2103126 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_rs262689:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AA AG GG GG GG GG GG AG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG AG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG

public/testdata/header.txt

@@ -1,14 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DBSNP129,Number=0,Type=Flag,Description="DBSNP129 Membership">
-##INFO=<ID=DBSNP132,Number=0,Type=Flag,Description="DBSNP132 Membership">
-##INFO=<ID=GenericAnnotation,Number=1,Type=Integer,Description="For each variant in the 'variants' ROD, finds all entries in the other -B files that overlap the variant's position.">
-##INFO=<ID=HAPMAP,Number=0,Type=Flag,Description="HAPMAP Membership">
-##INFO=<ID=OMNI,Number=0,Type=Flag,Description="OMNI Membership">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00513	NA12045	HG00625

public/testdata/indbnp129_notindbsnp132.txt

@@ -1 +0,0 @@
-20	10037119	.	G	.	469.85	PASS	AC=0;AF=0.00;AN=4;DBSNP129;DP=3;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.*811G>A;refseq.codingCoordStr_2=c.*811G>A;refseq.codingCoordStr_3=c.*811G>C;refseq.codingCoordStr_4=c.*811G>C;refseq.codingCoordStr_5=c.*811G>G;refseq.codingCoordStr_6=c.*811G>G;refseq.codingCoordStr_7=c.*811G>T;refseq.codingCoordStr_8=c.*811G>T;refseq.end_1=10037119;refseq.end_2=10037119;refseq.end_3=10037119;refseq.end_4=10037119;refseq.end_5=10037119;refseq.end_6=10037119;refseq.end_7=10037119;refseq.end_8=10037119;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=3535;refseq.mrnaCoord_2=3471;refseq.mrnaCoord_3=3535;refseq.mrnaCoord_4=3471;refseq.mrnaCoord_5=3535;refseq.mrnaCoord_6=3471;refseq.mrnaCoord_7=3535;refseq.mrnaCoord_8=3471;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr3;refseq.positionType_2=utr3;refseq.positionType_3=utr3;refseq.positionType_4=utr3;refseq.positionType_5=utr3;refseq.positionType_6=utr3;refseq.positionType_7=utr3;refseq.positionType_8=utr3;refseq.spliceDist_1=-289;refseq.spliceDist_2=-289;refseq.spliceDist_3=-289;refseq.spliceDist_4=-289;refseq.spliceDist_5=-289;refseq.spliceDist_6=-289;refseq.spliceDist_7=-289;refseq.spliceDist_8=-289;refseq.start_1=10037119;refseq.start_2=10037119;refseq.start_3=10037119;refseq.start_4=10037119;refseq.start_5=10037119;refseq.start_6=10037119;refseq.start_7=10037119;refseq.start_8=10037119;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:GQ:PL	./.	0/0:2:6:0,6,65	0/0:1:3:0,3,37

public/testdata/indbnp132_notindbsnp129.txt

@@ -1,2 +0,0 @@
-20	10015679	rs113024248	C	.	2829.33	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;OMNI	GT:DP:PL	./.	./.	./.
-20	10015790	rs114356776	G	.	43.60	PASS	AC=0;AF=0.00;AN=0;DBSNP132;DP=0;refseq.chr_1=20;refseq.chr_2=20;refseq.chr_3=20;refseq.chr_4=20;refseq.chr_5=20;refseq.chr_6=20;refseq.chr_7=20;refseq.chr_8=20;refseq.codingCoordStr_1=c.-300G>A;refseq.codingCoordStr_2=c.-236G>A;refseq.codingCoordStr_3=c.-300G>C;refseq.codingCoordStr_4=c.-236G>C;refseq.codingCoordStr_5=c.-300G>G;refseq.codingCoordStr_6=c.-236G>G;refseq.codingCoordStr_7=c.-300G>T;refseq.codingCoordStr_8=c.-236G>T;refseq.end_1=10015790;refseq.end_2=10015790;refseq.end_3=10015790;refseq.end_4=10015790;refseq.end_5=10015790;refseq.end_6=10015790;refseq.end_7=10015790;refseq.end_8=10015790;refseq.haplotypeAlternate_1=A;refseq.haplotypeAlternate_2=A;refseq.haplotypeAlternate_3=C;refseq.haplotypeAlternate_4=C;refseq.haplotypeAlternate_5=G;refseq.haplotypeAlternate_6=G;refseq.haplotypeAlternate_7=T;refseq.haplotypeAlternate_8=T;refseq.haplotypeReference_1=G;refseq.haplotypeReference_2=G;refseq.haplotypeReference_3=G;refseq.haplotypeReference_4=G;refseq.haplotypeReference_5=G;refseq.haplotypeReference_6=G;refseq.haplotypeReference_7=G;refseq.haplotypeReference_8=G;refseq.inCodingRegion_1=false;refseq.inCodingRegion_2=false;refseq.inCodingRegion_3=false;refseq.inCodingRegion_4=false;refseq.inCodingRegion_5=false;refseq.inCodingRegion_6=false;refseq.inCodingRegion_7=false;refseq.inCodingRegion_8=false;refseq.mrnaCoord_1=94;refseq.mrnaCoord_2=94;refseq.mrnaCoord_3=94;refseq.mrnaCoord_4=94;refseq.mrnaCoord_5=94;refseq.mrnaCoord_6=94;refseq.mrnaCoord_7=94;refseq.mrnaCoord_8=94;refseq.name2_1=ANKRD5;refseq.name2_2=ANKRD5;refseq.name2_3=ANKRD5;refseq.name2_4=ANKRD5;refseq.name2_5=ANKRD5;refseq.name2_6=ANKRD5;refseq.name2_7=ANKRD5;refseq.name2_8=ANKRD5;refseq.name_1=NM_022096;refseq.name_2=NM_198798;refseq.name_3=NM_022096;refseq.name_4=NM_198798;refseq.name_5=NM_022096;refseq.name_6=NM_198798;refseq.name_7=NM_022096;refseq.name_8=NM_198798;refseq.numMatchingRecords=8;refseq.positionType_1=utr5;refseq.positionType_2=utr5;refseq.positionType_3=utr5;refseq.positionType_4=utr5;refseq.positionType_5=utr5;refseq.positionType_6=utr5;refseq.positionType_7=utr5;refseq.positionType_8=utr5;refseq.spliceDist_1=94;refseq.spliceDist_2=94;refseq.spliceDist_3=94;refseq.spliceDist_4=94;refseq.spliceDist_5=94;refseq.spliceDist_6=94;refseq.spliceDist_7=94;refseq.spliceDist_8=94;refseq.start_1=10015790;refseq.start_2=10015790;refseq.start_3=10015790;refseq.start_4=10015790;refseq.start_5=10015790;refseq.start_6=10015790;refseq.start_7=10015790;refseq.start_8=10015790;refseq.transcriptStrand_1=+;refseq.transcriptStrand_2=+;refseq.transcriptStrand_3=+;refseq.transcriptStrand_4=+;refseq.transcriptStrand_5=+;refseq.transcriptStrand_6=+;refseq.transcriptStrand_7=+;refseq.transcriptStrand_8=+	GT:DP:PL	./.	./.	./.

public/testdata/indelAllelesForUG.vcf

@@ -1,43 +0,0 @@
-##fileformat=VCFv4.0
-##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
-##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
-##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
-##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
-##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">
-##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
-##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
-##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
-##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
-##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=[20:10,000,000-10,100,000] excludeIntervals=null reference_sequence=/humgen/1kg/reference/human_b36_both.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false enable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null quiet_output_mode=false debug_mode=false help=false genotype_likelihoods_model=DINDEL p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_mismatches_in_40bp_window=3 use_reads_with_bad_mates=false max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 insertionStartProbability=0.0010 insertionEndProbability=0.5 alphaDeletionProbability=0.0010 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=40.0 indelHaplotypeSize=80 indelDebug=true s1=null s2=null dovit=false newlike=false exactCalculation=LINEAR_EXPERIMENTAL output_all_callable_bases=false genotype=false out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub verbose_mode=null metrics_file=null annotation=[]"
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12878	NA19240
-20	10015049	.	TAAAAAAA	T	388.73	.	AC=3;AF=0.75;AN=4;DP=47;Dels=0.15;HRun=25;HaplotypeScore=18.5023;MQ=76.79;MQ0=9;QD=8.27;SB=-216.09;sumGLbyD=9.26	GT:AD:DP:GQ:PL	1/1:20,5:10:14.03:205,14,0	0/1:20,0:19:99:230,0,202
-20	10018938	.	G	GA	943.48	.	AC=3;AF=0.75;AN=4;DP=56;Dels=0.00;HRun=1;HaplotypeScore=8.3072;MQ=98.07;MQ0=0;QD=16.85;SB=-456.74;sumGLbyD=17.68	GT:AD:DP:GQ:PL	1/1:3,23:26:63.11:620,63,0	0/1:14,15:30:99:370,0,294
-20	10023508	.	GA	G	460.50	.	AC=2;AF=0.50;AN=4;DP=61;Dels=0.46;HRun=11;HaplotypeScore=9.7713;MQ=88.23;MQ0=1;QD=14.85;SB=-189.80;sumGLbyD=16.46	GT:AD:DP:GQ:PL	1/1:12,19:12:52.88:510,53,0	0/0:21,0:20:23.04:0,23,489
-20	10023669	.	GA	G	496.79	.	AC=2;AF=0.50;AN=4;DP=85;Dels=0.26;HRun=11;HaplotypeScore=15.0149;MQ=90.32;MQ0=0;QD=14.19;SB=-256.79;sumGLbyD=15.62	GT:AD:DP:GQ:PL	0/0:50,0:49:95.40:0,95,1160	1/1:13,22:13:61.87:547,62,0
-20	10025820	.	TC	T	381.82	.	AC=2;AF=0.50;AN=4;DP=65;Dels=0.25;HRun=1;HaplotypeScore=7.8208;MQ=83.23;MQ0=4;QD=20.10;SB=-190.53;sumGLbyD=22.72	GT:AD:DP:GQ:PL	0/0:46,0:44:99:0,120,2093	1/1:3,16:0:47.55:432,48,0
-20	10026897	.	T	TA	189.77	.	AC=2;AF=0.50;AN=4;DP=38;Dels=0.00;HRun=8;HaplotypeScore=5.5665;MQ=83.15;MQ0=0;QD=15.81;SB=-97.18;sumGLbyD=19.96	GT:AD:DP:GQ:PL	0/0:26,0:26:54.12:0,54,562	1/1:3,9:12:23:239,23,0
-20	10027761	.	T	TAA	1185.09	.	AC=2;AF=0.50;AN=4;DP=53;Dels=0.00;HRun=0;HaplotypeScore=7.3429;MQ=96.45;MQ0=0;QD=59.25;SB=-568.38;sumGLbyD=61.75	GT:AD:DP:GQ:PL	0/0:33,0:33:89.29:0,89,1077	1/1:1,16:20:54.58:1235,55,0
-20	10036968	.	C	CAAA	354.48	.	AC=3;AF=0.75;AN=4;DP=40;Dels=0.00;HRun=11;HaplotypeScore=4.0302;MQ=77.44;MQ0=1;QD=8.86;SB=-0.00;sumGLbyD=10.03	GT:AD:DP:GQ:PL	0/1:22,1:23:96.54:97,0,232	1/1:10,4:13:18.02:305,18,0
-20	10038289	.	CAA	C	229.65	.	AC=2;AF=0.50;AN=4;DP=44;Dels=0.23;HRun=16;HaplotypeScore=10.5739;MQ=86.96;MQ0=0;QD=5.22;SB=-82.31;sumGLbyD=6.21	GT:AD:DP:GQ:PL	0/1:19,3:19:42.22:42,0,276	0/1:15,5:14:24.06:231,0,24
-20	10041568	.	GT	G	32.14	.	AC=1;AF=0.25;AN=4;DP=178;Dels=0.03;HRun=13;HaplotypeScore=99.6777;MQ=38.37;MQ0=88;QD=0.64;SB=-15.66;sumGLbyD=1.43	GT:AD:DP:GQ:PL	0/1:43,6:20:71.38:71,0,253	0/0:126,0:20:2.40:1,0,250
-20	10044905	.	TA	T	684.30	.	AC=3;AF=0.75;AN=4;DP=49;Dels=0.55;HRun=2;HaplotypeScore=6.7735;MQ=82.97;MQ0=0;QD=13.97;SB=-102.02;sumGLbyD=14.92	GT:AD:DP:GQ:PL	0/1:22,10:22:99:217,0,579	1/1:0,17:0:51.04:514,51,0
-20	10045101	.	C	CTTTT	382.10	.	AC=3;AF=0.75;AN=4;DP=33;Dels=0.00;HRun=10;HaplotypeScore=4.5637;MQ=76.02;MQ0=0;QD=11.58;SB=-102.18;sumGLbyD=12.98	GT:AD:DP:GQ:PL	0/1:12,0:12:6.91:7,0,476	1/1:12,6:21:25.29:422,25,0
-20	10048539	.	CTTCTAG	C	2079.87	.	AC=3;AF=0.75;AN=4;DP=46;Dels=0.63;HRun=0;HaplotypeScore=3.9254;MQ=91.40;MQ0=0;QD=45.21;SB=-843.04;sumGLbyD=46.23	GT:AD:DP:GQ:PL	0/1:13,9:13:99:518,0,828	1/1:4,20:3:59.77:1608,60,0
-20	10049268	.	TAA	T	713.22	.	AC=3;AF=0.75;AN=4;DP=49;Dels=0.47;HRun=7;HaplotypeScore=8.7440;MQ=85.12;MQ0=1;QD=14.56;SB=-335.96;sumGLbyD=15.51	GT:AD:DP:GQ:PL	0/1:24,6:22:99:206,0,1109	1/1:2,17:1:49.97:554,50,0
-20	10049674	.	TTGTGTGTGTGTG	T	514.36	.	AC=1;AF=0.25;AN=4;DP=58;Dels=0.14;HRun=0;HaplotypeScore=12.9192;MQ=71.13;MQ0=10;QD=14.29;SB=-160.31;sumGLbyD=15.55	GT:AD:DP:GQ:PL	0/0:22,0:17:15.05:0,15,459	0/1:28,8:17:1.62:558,3,0
-20	10055047	.	AG	A	384.31	.	AC=1;AF=0.25;AN=4;DP=63;Dels=0.27;HRun=1;HaplotypeScore=6.3278;MQ=88.56;MQ0=0;QD=13.25;SB=-169.84;sumGLbyD=14.70	GT:AD:DP:GQ:PL	0/1:12,17:12:99:426,0,486	0/0:34,0:32:92.56:0,93,1711
-20	10055331	.	G	GTT	1154.63	.	AC=3;AF=0.75;AN=4;DP=59;Dels=0.00;HRun=12;HaplotypeScore=11.0007;MQ=93.08;MQ0=0;QD=19.57;SB=-596.65;sumGLbyD=20.36	GT:AD:DP:GQ:PL	0/1:22,3:26:99:157,0,321	1/1:11,20:31:57.17:1045,57,0
-20	10058726	.	GT	G	519.26	.	AC=3;AF=0.75;AN=4;DP=48;Dels=0.54;HRun=5;HaplotypeScore=3.4082;MQ=90.03;MQ0=0;QD=10.82;SB=-101.29;sumGLbyD=11.79	GT:AD:DP:GQ:PL	0/1:19,8:18:99:132,0,487	1/1:3,18:3:45.97:434,46,0
-20	10062705	.	CA	C	358.95	.	AC=2;AF=0.50;AN=4;DP=60;Dels=0.33;HRun=12;HaplotypeScore=11.1474;MQ=88.71;MQ0=0;QD=5.98;SB=-176.95;sumGLbyD=6.71	GT:AD:DP:GQ:PL	0/1:21,5:20:46.82:47,0,450	0/1:19,15:18:99:356,0,162
-20	10068207	.	C	CAGGCCACAA	477.12	.	AC=2;AF=0.50;AN=4;DP=54;Dels=0.00;HRun=0;HaplotypeScore=26.9189;MQ=93.42;MQ0=0;QD=8.84;SB=-243.75;sumGLbyD=9.65	GT:AD:DP:GQ:PL	0/1:20,1:26:99:245,0,1438	0/1:28,0:28:99:276,0,1441
-20	10069161	.	T	TA	75.14	.	AC=1;AF=0.25;AN=4;DP=73;Dels=0.03;HRun=10;HaplotypeScore=6.3510;MQ=92.42;MQ0=0;QD=2.59;SB=-46.22;sumGLbyD=4.04	GT:AD:DP:GQ:PL	0/0:42,0:42:97.19:0,97,941	0/1:22,6:28:99:117,0,324
-20	10076619	.	CTTTGT	C	980.18	.	AC=1;AF=0.25;AN=4;DP=54;Dels=0.26;HRun=0;HaplotypeScore=6.3555;MQ=89.08;MQ0=0;QD=35.01;SB=-226.12;sumGLbyD=36.51	GT:AD:DP:GQ:PL	0/0:26,0:26:63.22:0,63,1916	0/1:14,14:14:99:1022,0,1081
-20	10078345	.	G	GTA	764.75	.	AC=3;AF=0.75;AN=4;DP=38;Dels=0.00;HRun=0;HaplotypeScore=7.6113;MQ=83.32;MQ0=0;QD=20.13;SB=-141.91;sumGLbyD=21.36	GT:AD:DP:GQ:PL	0/1:14,3:17:99:125,0,213	1/1:8,10:19:30.10:687,30,0

public/testdata/indels.txt

@@ -1 +0,0 @@
-20	4680094	rs112637437	CCATGGTGGTGGCTGGGGACAGCCT	C	3590.76	.	AC=12;AF=0.0625;AN=192;DB;DP=1386;Dels=0.04;HRun=1;HaplotypeScore=3.9792;MQ=57.75;MQ0=6;QD=21.89;SB=-1275.83;sumGLbyD=21.89	GT:DP:GQ:PL	0/0:28:51.14:0,51,1539	0/1:8:99:287,0,160	0/1:10:99:549,0,338

public/testdata/inhapmap.txt

@@ -1 +0,0 @@
-20	10047435	rs598275	G	A	82495.04	PASS	AC=6;AF=1.00;AN=6;DBSNP129;DBSNP132;DP=8;HAPMAP;OMNI	GT:DP:GQ:PL	1/1:2:6:69,6,0	1/1:2:6:69,6,0	1/1:4:12:139,12,0