**30**wrote:

hi, everyone! I am working on illumina pair-end sequencing

After mapping by bwa, I got a pair of reads with MAPQ=0, with both reads mapped to more than one place. But the Template Length is OK, and I find this pair of reads in this sam file only once.

So, should we dump this mapping pair?

SPECIFIC_ID 83 Y 58900709 0 92M = 58900679 -122 AGTGCATTCCATTCCAGTCTCTTCAGTTCGATTCCATTCCATTCGTTTCGATTCCTTTCCATTCCAGCCCATTCCATTCCATTGCATTCCTT DDDCDCDDD DDDDDDDDDDDDEEC?FFFFFHHHHHJJIJIHJIJJJJIJJJJJJIJHGJJIHFJJJIGIJJIHIJIJHJJIJJIJJIFHFFH XT:A:R NM:i:1 SM:i:0 AM:i:0 X0 :i:9 X1:i:16 XM:i:1 XO:i:0 XG:i:0 MD:Z:83C8 :i:9 X1:i:16 XM:i:1 XO:i:0 XG:i:0 MD:Z:83C8

SPECIFIC_ID 163 Y 58900679 0 92M = 58900709 122 AGAACCTTCCATTACACTCCCTTCCATTCCAGTGCATTCCATTCCAGTCTCTTCAGTTCGATTCCATTCCATTCGTTTCGATTCCTTTCCAT FHGHHIIJJ JGJIIJIJJIIJJIIJEIGEGHIIJJIJIGIIIF<fgiijjhjieejijiiijhehehigggghegghjc=ehf@deef?>CD XT:A:R NM:i:0 SM:i:0 AM:i:0 X0 :i:2 X1:i:18 XM:i:0 XO:i:0 XG:i:0 MD:Z:92

Thanks very much!

**2.6k**• written 6.7 years ago by PeterPan •

**30**