Why do I have more reads in my .bam file than in my .fastq input file?

Question

[francois]

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?

[cpad0112]

Please post entire log from flagstat @op

[lakhujanivijay]

Had the same question couple of years ago!

Answer 1

[Pierre Lindenbaum]

the bam contains the supplementary (part of the read that maps elsewhere) + secondary (some other probable hits for the read) alignments