diff --git a/src/sam/markdups/pipeline_md.cpp b/src/sam/markdups/pipeline_md.cpp
index 5877929..d731f76 100644
--- a/src/sam/markdups/pipeline_md.cpp
+++ b/src/sam/markdups/pipeline_md.cpp
@@ -322,20 +322,17 @@ static inline void refreshPairDupIdx(DPSet<DupInfo> &dupIdx, MDSet<int64_t> &opt
 
 // 用来分别处理dup和optical dup
 static void refeshTaskDupInfo(DPSet<DupInfo> &dupIdx, MDSet<int64_t> &opticalDupIdx, DPSet<DupInfo> &repIdx,
-                              MDSet<int64_t> &singletonIdx, MDSet<int64_t> &notDupIdx, MDSet<int64_t> &notOpticalDupIdx,
-                              MDSet<int64_t> &notRepIdx, MDSet<int64_t> &notSingletonIdx, DPSet<DupInfo> &latterDupIdx,
+                              MDSet<int64_t> &notDupIdx, MDSet<int64_t> &notOpticalDupIdx, MDSet<int64_t> &notRepIdx,
+                              MDSet<int64_t> &notSingletonIdx, DPSet<DupInfo> &latterDupIdx,
                               MDSet<int64_t> &latterOpticalDupIdx, DPSet<DupInfo> &latterRepIdx,
-                              MDSet<int64_t> &latterSingletonIdx, MDSet<int64_t> &latterNotDupIdx,
-                              MDSet<int64_t> &latterNotOpticalDupIdx, MDSet<int64_t> &latterNotRepIdx,
-                              MDSet<int64_t> &latterNotSingletonIdx) {
+                              MDSet<int64_t> &latterNotDupIdx, MDSet<int64_t> &latterNotOpticalDupIdx,
+                              MDSet<int64_t> &latterNotRepIdx) {
     for (auto idx : dupIdx) latterDupIdx.insert(idx);
     for (auto idx : opticalDupIdx) latterOpticalDupIdx.insert(idx);
     for (auto idx : repIdx) latterRepIdx.insert(idx);
-    for (auto idx : singletonIdx) latterSingletonIdx.insert(idx);
     for (auto idx : notDupIdx) latterNotDupIdx.insert(idx);
     for (auto idx : notOpticalDupIdx) latterNotOpticalDupIdx.insert(idx);
     for (auto idx : notRepIdx) latterNotRepIdx.insert(idx);
-    for (auto idx : notSingletonIdx) latterNotSingletonIdx.insert(idx);
 }
 
 /* 最后合并数据并排序 */
@@ -506,7 +503,6 @@ static void doMarkDup(PipelineArg &pipeArg) {
     mdData.pairDupIdx.clear();
     mdData.pairOpticalDupIdx.clear();
     mdData.pairRepIdx.clear();
-    mdData.pairSingletonIdx.clear();
 
     tm_arr[5].acc_start();
     auto tmpPtr = mdData.dataPtr;
@@ -516,7 +512,7 @@ static void doMarkDup(PipelineArg &pipeArg) {
     SortMarkData &smd = *(SortMarkData *)mdData.dataPtr;
     //  先处理 pair
     processPairs(smd.pairs, &mdData.pairDupIdx, &mdData.pairOpticalDupIdx, &mdData.pairRepIdx,
-                 &mdData.pairSingletonIdx);
+                 nullptr);
     // 再处理frag
     processFrags(smd.frags, &mdData.fragDupIdx);
 }
@@ -543,12 +539,10 @@ static void refreshMarkDupData(DPSet<DupInfo> &dupIdx, MDSet<int64_t> &opticalDu
     refreshDupIdx(dupIdx, lp.pairDupIdx, p.pairDupIdx);
     refreshDupIdx(opticalDupIdx, lp.pairOpticalDupIdx, p.pairOpticalDupIdx);
     refreshDupIdx(repIdx, lp.pairRepIdx, p.pairRepIdx);
-    refreshDupIdx(singletonIdx, lp.pairSingletonIdx, p.pairSingletonIdx);
 
     refreshNotDupIdx(notDupIdx, lp.pairDupIdx, p.pairDupIdx);
     refreshNotDupIdx(notOpticalDupIdx, lp.pairOpticalDupIdx, p.pairOpticalDupIdx);
     refreshNotDupIdx(notRepIdx, lp.pairRepIdx, p.pairRepIdx);
-    refreshNotDupIdx(notSingletonIdx, lp.pairSingletonIdx, p.pairSingletonIdx);
 }
 
 // for step-5 sort
@@ -751,12 +745,10 @@ static void doIntersect(PipelineArg &pipeArg) {
         auto taskSeq = e.first;
         auto &t = e.second;
         if (taskSeq < lp.taskSeq) {
-            refeshTaskDupInfo(t.dupIdx, t.opticalDupIdx, t.repIdx, t.singletonIdx, t.notDupIdx, t.notOpticalDupIdx,
-                              t.notRepIdx, t.notSingletonIdx, g.latterDupIdxArr[taskSeq],
-                              g.latterOpticalDupIdxArr[taskSeq], g.latterRepIdxArr[taskSeq],
-                              g.latterSingletonIdxArr[taskSeq], g.latterNotDupIdxArr[taskSeq],
-                              g.latterNotOpticalDupIdxArr[taskSeq], g.latterNotRepIdxArr[taskSeq],
-                              g.latterNotSingletonIdxArr[taskSeq]);
+            refeshTaskDupInfo(t.dupIdx, t.opticalDupIdx, t.repIdx, t.notDupIdx, t.notOpticalDupIdx, t.notRepIdx,
+                              t.notSingletonIdx, g.latterDupIdxArr[taskSeq], g.latterOpticalDupIdxArr[taskSeq],
+                              g.latterRepIdxArr[taskSeq], g.latterNotDupIdxArr[taskSeq],
+                              g.latterNotOpticalDupIdxArr[taskSeq], g.latterNotRepIdxArr[taskSeq]);
         } else if (taskSeq == lp.taskSeq) {
             refreshMarkDupData(t.dupIdx, t.opticalDupIdx, t.repIdx, t.singletonIdx, t.notDupIdx, t.notOpticalDupIdx,
                                t.notRepIdx, t.notSingletonIdx, lp, p);
@@ -1033,11 +1025,10 @@ static void mergeAllTask(PipelineArg &pipeArg) {
     for (auto &e : taskChanged) {
         auto taskSeq = e.first;
         auto &t = e.second;
-        refeshTaskDupInfo(t.dupIdx, t.opticalDupIdx, t.repIdx, t.singletonIdx, t.notDupIdx, t.notOpticalDupIdx,
-                          t.notRepIdx, t.notSingletonIdx, g.latterDupIdxArr[taskSeq], g.latterOpticalDupIdxArr[taskSeq],
-                          g.latterRepIdxArr[taskSeq], g.latterSingletonIdxArr[taskSeq], g.latterNotDupIdxArr[taskSeq],
-                          g.latterNotOpticalDupIdxArr[taskSeq], g.latterNotRepIdxArr[taskSeq],
-                          g.latterNotSingletonIdxArr[taskSeq]);
+        refeshTaskDupInfo(t.dupIdx, t.opticalDupIdx, t.repIdx, t.notDupIdx, t.notOpticalDupIdx, t.notRepIdx,
+                          t.notSingletonIdx, g.latterDupIdxArr[taskSeq], g.latterOpticalDupIdxArr[taskSeq],
+                          g.latterRepIdxArr[taskSeq], g.latterNotDupIdxArr[taskSeq],
+                          g.latterNotOpticalDupIdxArr[taskSeq], g.latterNotRepIdxArr[taskSeq]);
     }
     g.unpairedPosArr.clear();
 
diff --git a/src/sam/markdups/pipeline_md.h b/src/sam/markdups/pipeline_md.h
index 47859d6..8e48a5d 100644
--- a/src/sam/markdups/pipeline_md.h
+++ b/src/sam/markdups/pipeline_md.h
@@ -42,7 +42,6 @@ struct MarkDupData {
     MDSet<int64_t> pairOpticalDupIdx;  // optical冗余read的索引
     DPSet<DupInfo> fragDupIdx;         // frag的冗余read的索引
     DPSet<DupInfo> pairRepIdx;         // pair的dupset代表read的索引
-    MDSet<int64_t> pairSingletonIdx;   // 某位置只有一对read的所有read pair个数
 
     volatile void *dataPtr;  // SortMarkData pointer
 };
@@ -55,17 +54,14 @@ struct IntersectData {
     vector<vector<DupInfo>> dupIdxArr;
     vector<vector<int64_t>> opticalDupIdxArr;
     vector<vector<DupInfo>> repIdxArr;
-    vector<vector<int64_t>> singletonIdxArr;
 
     // 用来存放后续计算的数据
     vector<DPSet<DupInfo>> latterDupIdxArr;
     vector<MDSet<int64_t>> latterOpticalDupIdxArr;
     vector<DPSet<DupInfo>> latterRepIdxArr;
-    vector<MDSet<int64_t>> latterSingletonIdxArr;
     vector<MDSet<int64_t>> latterNotDupIdxArr;
     vector<MDSet<int64_t>> latterNotOpticalDupIdxArr;
     vector<MDSet<int64_t>> latterNotRepIdxArr;
-    vector<MDSet<int64_t>> latterNotSingletonIdxArr;
 };
 
 // 记录流水线状态，task的序号，以及某阶段是否结束