title: Three reads with the same name in the BAM file
body: <p>I am dealing with the paired-end BAM file, and come up with many warnings like this: </p>
  
  <pre><code>WARNING: Could not find pair for HWI-ST430:177:2:1:4979:15503#0
  WARNING: Could not find pair for HWI-ST430:177:2:1:5127:13427#0
  WARNING: Could not find pair for HWI-ST430:177:2:1:6521:21452#0
  </code></pre>
  
  <p>I check the warning reads in the BAM file, and find all the warning reads have three reads with the same name. For example:</p>
  
  <pre><code>HWI-ST430:177:2:1:4979:15503#0  65  chr32   26100696    60  79M21S  chr5    36697147    0   ACTTTGCAATTTAAGTTTTACTTACTTTTTAACTAATATACATGCCTAAAATTTACAAAAACAATAATAAAAACAACAGAACACTGGAAACATTTTTAAA    &gt;;=&lt;&gt;=&lt;&lt;=======&lt;====;===;=======&lt;=&gt;&gt;&gt;&gt;&gt;&gt;&lt;=&gt;&gt;==&gt;&gt;&gt;&gt;=&gt;&gt;&gt;&gt;==&gt;?&gt;=&lt;&lt;==&gt;?&gt;&gt;&gt;?&gt;?==&gt;&lt;=?&gt;&gt;&lt;=&lt;&gt;&gt;&gt;?&gt;?=&gt;??&gt;?===&gt;    BD:Z:FFHFCIKKIHG@EEEHF??DGGEDGGE???DEEGGEFFFFGDHHHHGGE??FF?DGDG???EDGFGFGGF@@@FEHFEIEGFEEIJJIHBHGLJDD@EF@   MD:Z:79 PG:Z:MarkDuplicates RG:Z:Basenji    BI:Z:FFIECHGIHFEAFEEHEAAFFHDFFHDAAAFEEIHFGGHGGGHHGHHHFBBGFBGGGHBBBFGHGGFGGFBBBGHIGHJGHGHFKJJJJEIKLJGHBGFB   NM:i:0  AS:i:79 XS:i:19
  HWI-ST430:177:2:1:4979:15503#0  129 chr5    36697147    60  72M28S  chr32   26100696    0   ATTTGCCCCTGGGCTATTTTTTTCCTNCCATGTAAGATTCCGTTTTAAAAATGTTTCCAGTGTTCTGTTGTTTTTATTATTGTTTTTGTAAATTTTAGGC    ===&lt;=&lt;&lt;&lt;&lt;====&lt;=&gt;========&lt;&lt;!&lt;&lt;&lt;=&gt;&lt;&lt;=&gt;&gt;&gt;&gt;&gt;=5=&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;=&gt;&gt;&gt;==&gt;=&gt;=&gt;&gt;&gt;&gt;=?&gt;=&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;=?&gt;=&gt;&gt;&gt;?&gt;&gt;&gt;??&gt;??&gt;;&lt;=&gt;    SA:Z:chr32,26100739,-,36M64S,60,0;  BD:Z:FFG@JKKFFHIIEHIGFF?????EGGEEEGHHEGEEDGFEGEGF??DE???FHEF?EGGHIFFGFEIFGGFG@@@EGGEGGGFHAAAHGJHBJJDDEHHI   MD:Z:26T37T7    PG:Z:MarkDuplicates RG:Z:Basenji    BI:Z:FFFBHHHFFHGGDGHGGEAAAAADFGEEEIHHGHFFFGFEGHHFBBGFBBBGHGFBEGIIIFGFEFHGFHHGCCCHIGHIGHHGDDDIIKIFKJGHGHGH   NM:i:2  AS:i:65 XS:i:21
  HWI-ST430:177:2:1:4979:15503#0  401 chr32   26100739    60  36M64H  =   26100696    -79 GCCTAAAATTTACAAAAACAATAATAAAAACAACAG    ===&lt;=&gt;&gt;=&gt;&gt;===&gt;===&lt;=&gt;===========&gt;;===    SA:Z:chr5,36697147,+,72M28S,60,2;   BD:Z:IHHE??FF?EGEF???FEFFFDFGE@@AHHIJFIFF   MD:Z:36 PG:Z:MarkDuplicates RG:Z:Basenji    BI:Z:HGHGBBFFAEGFFAAAEFFEGFEGFABBFGHGGHFF   NM:i:0  AS:i:36 XS:i:22
  </code></pre>
  
  <p>The BAM file is alignment of HiSeq reads aligned to the reference genome using bwa, and use picard to remove redundancy. Base realignments were done using gatk.</p>
  
  <p>My confusion is:</p>
  
  <p>1、Why there are three reads with the same name, but have no relation?</p>
  
  <p>2、Maybe the first two are treated as mate pairs and the third as a single read. So could I just ignore it?</p>
  
  <p>Could eveyone help me? Many thanks for your help!</p>