diff --git a/src/bqsr/apply_bqsr_entry.cpp b/src/bqsr/apply_bqsr_entry.cpp
index fa9dec0..806f9f4 100644
--- a/src/bqsr/apply_bqsr_entry.cpp
+++ b/src/bqsr/apply_bqsr_entry.cpp
@@ -73,11 +73,13 @@ int SerialApplyBQSR(AuxVar &aux) {
 
         // 二. 遍历每个bam（read）记录，进行处理
         for (int i = 0; i < bams.size(); ++i) {
+            BamWrap *bw = bams[i];
+
             if (bam_copy1(recalBams[i], bams[i]->b) == NULL) {
                 spdlog::error("Copy bam error");
                 exit(1);
             }
-            BamWrap* bw = bams[i];
+            // BamWrap* bw = bams[i];
             bw->b = recalBams[i]; // 注意这里的赋值，然后就可以对b进行更改了
             sd.init();
             sd.parseForApplyBQSR(bw);
@@ -151,6 +153,12 @@ int SerialApplyBQSR(AuxVar &aux) {
                 recalibratedQuals[offset] = quantizedQualityScore;
             }
 
+            // fprintf(gf[4], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
+            // for (size_t si = 0; si < sd.read_len; ++si) {
+            //     fprintf(gf[4], "%d ", (int)recalibratedQuals[si]);
+            // }
+            // fprintf(gf[4], "\n");
+
             if (sam_write1(nsgv::gOutBamFp, nsgv::gOutBamHeader, bw->b) < 0) {
                 spdlog::error("failed writing sam record to \"{}\"", nsgv::gBqsrArg.OUTPUT_FILE.c_str());
                 sam_close(nsgv::gInBamFp);
diff --git a/src/bqsr/recal_datum.h b/src/bqsr/recal_datum.h
index 2339c25..04c06e6 100644
--- a/src/bqsr/recal_datum.h
+++ b/src/bqsr/recal_datum.h
@@ -159,6 +159,7 @@ struct RecalDatum {
      */
     double getEmpiricalQuality() { return getEmpiricalQuality(getReportedQuality()); }
     inline void setEmpiricalQuality(double val) { empiricalQuality = val; }
+    inline void setEmpiricalQuality(int val) { empiricalQuality = val; }
 
     /**
      * Computes the empirical base quality (roughly (num errors)/(num observations)) from the counts stored in this datum.
diff --git a/src/bqsr/recal_utils.h b/src/bqsr/recal_utils.h
index 15ad673..febde7a 100644
--- a/src/bqsr/recal_utils.h
+++ b/src/bqsr/recal_utils.h
@@ -399,7 +399,8 @@ struct RecalUtils {
             int k2 = ReadGroupCovariate::RgToId[dats[i][0]];
             int k1 = EventType::GetIndexForEventRep(dats[i][1][0]);
             auto& datum = recalTables.readGroupTable(k1, k2);
-            datum.setEmpiricalQuality(ReportUtil::ToDouble(dats[i][2]));
+            // datum.setEmpiricalQuality(ReportUtil::ToDouble(dats[i][2]));  // 这个数值在GATK4里是需要重新计算的
+            datum.setEmpiricalQuality(RecalDatum::UNINITIALIZED_EMPIRICAL_QUALITY);
             datum.setReportedQuality(ReportUtil::ToDouble(dats[i][3]));
             datum.setNumObservations(ReportUtil::ToUint64(dats[i][4]));
             datum.setNumMismatches(ReportUtil::ToDouble(dats[i][5]));
@@ -425,7 +426,8 @@ struct RecalUtils {
             int k3 = ReportUtil::ToInt(dat[1]);
             int k1 = EventType::GetIndexForEventRep(dat[2][0]);
             auto& datum = recalTables.qualityScoreTable(k1, k2, k3);
-            datum.setEmpiricalQuality(ReportUtil::ToDouble(dat[3]));
+            // datum.setEmpiricalQuality(ReportUtil::ToDouble(dat[3]));  // 这个数值在GATK4里是需要重新计算的
+            datum.setEmpiricalQuality(RecalDatum::UNINITIALIZED_EMPIRICAL_QUALITY);
             datum.setReportedQuality((double)k3);
             datum.setNumObservations(ReportUtil::ToUint64(dat[4]));
             datum.setNumMismatches(ReportUtil::ToDouble(dat[5]));
@@ -461,7 +463,8 @@ struct RecalUtils {
             } else {
                 spdlog::error("Unknown CovariateName {}", dat[3]);
             }
-            dp->setEmpiricalQuality(ReportUtil::ToDouble(dat[5]));
+            // dp->setEmpiricalQuality(ReportUtil::ToDouble(dat[5])); // 这个数值在GATK4里是需要重新计算的
+            dp->setEmpiricalQuality(RecalDatum::UNINITIALIZED_EMPIRICAL_QUALITY);  // 这个数值在GATK4里是需要重新计算的
             dp->setReportedQuality((double)k3);
             dp->setNumObservations(ReportUtil::ToUint64(dat[6]));
             dp->setNumMismatches(ReportUtil::ToDouble(dat[7]));