Hi,
I got the following info after running a samtools flagstat on a Novoalign bam file:
126597089 in total
0 QC failure
0 duplicates
122446987 mapped (96.72%)
126597089 paired in sequencing
63372478 read1
63224611 read2
104053862 properly paired (82.19%)
118953502 with itself and mate mapped
3493485 singletons (2.76%)
14745930 with mate mapped to a different chr
8838136 with mate mapped to a different chr (mapQ>=5)
what does the line no. 5 signify? and since these are paired reads, shouldn't read1 and read2 numbers be the same? does it have anything to do with using the "-r A" option for sam generation?
Thanks in advance.
I got the following info after running a samtools flagstat on a Novoalign bam file:
126597089 in total
0 QC failure
0 duplicates
122446987 mapped (96.72%)
126597089 paired in sequencing
63372478 read1
63224611 read2
104053862 properly paired (82.19%)
118953502 with itself and mate mapped
3493485 singletons (2.76%)
14745930 with mate mapped to a different chr
8838136 with mate mapped to a different chr (mapQ>=5)
what does the line no. 5 signify? and since these are paired reads, shouldn't read1 and read2 numbers be the same? does it have anything to do with using the "-r A" option for sam generation?
Thanks in advance.
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