Why do I have more reads in my .bam file than in my .fastq input file?
I seem to have more reads after alignment than before.
Before alignment
awk '{s++}END{print s/4}' reads.fastq
153265
After alignment
samtools flagstat align.bam
180051 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
26786 + 0 supplementary
0 + 0 duplicates
171567 + 0 mapped (95.29% : N/A)
[...]
I do not understand how can that be.
Can you help?
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Pierre Lindenbaum
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francois •
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francois •
1 answer
the bam contains the supplementary (part of the read that maps elsewhere) + secondary (some other probable hits for the read) alignments
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Pierre Lindenbaum
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Please post entire log from flagstat @op
Had the same question couple of years ago!