#:GATKReport.v1.1:5
#:GATKTable:11:3:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%.2f
#:GATKTable:CompOverlap:The overlap between eval and comp sites
CompOverlap  CompRod  EvalRod  JexlExpression  Novelty  nEvalVariants  novelSites  nVariantsAtComp  compRate  nConcordant  concordantRate
CompOverlap  dbsnp    eval     none            all                481          12              469     97.51          468           99.79
CompOverlap  dbsnp    eval     none            known              469           0              469    100.00          468           99.79
CompOverlap  dbsnp    eval     none            novel               12          12                0      0.00            0            0.00

#:GATKTable:30:3:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%.2e:%.2f:%.2f:%.2e:%.2f:%.2f
#:GATKTable:CountVariants:Counts different classes of variants in the sample
CountVariants  CompRod  EvalRod  JexlExpression  Novelty  nProcessedLoci  nCalledLoci  nRefLoci  nVariantLoci  variantRate            variantRatePerBp  nSNPs  nMNPs  nInsertions  nDeletions  nComplex  nSymbolic  nMixed  nNoCalls  nHets  nHomRef  nHomVar  nSingletons  nHomDerived  heterozygosity  heterozygosityPerBp  hetHomRatio  indelRate  indelRatePerBp  deletionInsertionRatio
CountVariants  dbsnp    eval     none            all            63025520          481         0           481    7.63182913841885E-6          131030.0    481      0            0           0         0          0       0         0    298        0      183          298            0        4.73e-06            211495.00         1.63   0.00e+00            0.00                    0.00
CountVariants  dbsnp    eval     none            known          63025520          469         0           469   7.441430074674513E-6          134382.0    469      0            0           0         0          0       0         0    288        0      181          288            0        4.57e-06            218838.00         1.59   0.00e+00            0.00                    0.00
CountVariants  dbsnp    eval     none            novel          63025520           12         0            12  1.9039906374433722E-7         5252126.0     12      0            0           0         0          0       0         0     10        0        2           10            0        1.59e-07           6302552.00         5.00   0.00e+00            0.00                    0.00

#:GATKTable:14:3:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%s:%.2f:%s:%s:%.2f
#:GATKTable:TiTvVariantEvaluator:Ti/Tv Variant Evaluator
TiTvVariantEvaluator  CompRod  EvalRod  JexlExpression  Novelty  nTi  nTv  tiTvRatio  nTiInComp  nTvInComp  TiTvRatioStandard  nTiDerived  nTvDerived  tiTvDerivedRatio
TiTvVariantEvaluator  dbsnp    eval     none            all      382   99       3.86     203506      85497               2.38           0           0              0.00
TiTvVariantEvaluator  dbsnp    eval     none            known    374   95       3.94        360         91               3.96           0           0              0.00
TiTvVariantEvaluator  dbsnp    eval     none            novel      8    4       2.00     203146      85406               2.38           0           0              0.00

#:GATKTable:24:3:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%.2f:%.2f:%.2f:%s:%s:%s:%s:%s:%s:%s:%s:%s:%s
#:GATKTable:ValidationReport:Assess site accuracy and sensitivity of callset against follow-up validation assay
ValidationReport  CompRod  EvalRod  JexlExpression  Novelty  nComp   TP   FP  FN      TN  sensitivity  specificity  PPV     FDR   CompMonoEvalNoCall  CompMonoEvalFiltered  CompMonoEvalMono  CompMonoEvalPoly  CompPolyEvalNoCall  CompPolyEvalFiltered  CompPolyEvalMono  CompPolyEvalPoly  CompFiltered  nDifferentAlleleSites
ValidationReport  dbsnp    eval     none            all      369102  469   0  368633   0         0.13       100.00  100.00  0.00                   0                     0                 0                 0              368633                     0                 0               469             0                      0
ValidationReport  dbsnp    eval     none            known       469  469   0       0   0       100.00       100.00  100.00  0.00                   0                     0                 0                 0                   0                     0                 0               469             0                      0
ValidationReport  dbsnp    eval     none            novel    368633    0   0  368633   0         0.00       100.00     NaN   NaN                   0                     0                 0                 0              368633                     0                 0                 0             0                      0

#:GATKTable:20:3:%s:%s:%s:%s:%s:%s:%s:%s:%.2f:%s:%s:%.2f:%.1f:%s:%s:%s:%.1f:%s:%s:%s
#:GATKTable:VariantSummary:1000 Genomes Phase I summary of variants table
VariantSummary  CompRod  EvalRod  JexlExpression  Novelty  nSamples  nProcessedLoci  nSNPs  TiTvRatio  SNPNoveltyRate  nSNPsPerSample  TiTvRatioPerSample  SNPDPPerSample  nIndels  IndelNoveltyRate  nIndelsPerSample  IndelDPPerSample  nSVs  SVNoveltyRate  nSVsPerSample
VariantSummary  dbsnp    eval     none            all             1        63025520    481       3.86            0.02             481                3.86           481.0        0                NA                 0               0.0     0             NA              0
VariantSummary  dbsnp    eval     none            known           1        63025520    469       3.94            0.00             469                3.94           469.0        0                NA                 0               0.0     0             NA              0
VariantSummary  dbsnp    eval     none            novel           1        63025520     12       2.00            1.00              12                2.00            12.0        0                NA                 0               0.0     0             NA              0

