why my WGS bam file (after alignment) shows more reads than the starting fastq file

Question

[maria2019]

I have one paired ended (150x2) WGS fastq file.

fastqc QC total read = ~ 459 M

fastqc QC after trimming total reads = ~ 458 M

after the alignment with bwa-mem and realigning around the indel, I used QUALIMAP for QC and the report shows ~723 M reads!

Why do I get more reads after the alignment?

[yzliu01]

I am having the same issue. The total number of reads is even larger in the bam file generated with filted fastq file than the raw fastq file. Do you know why it happened like this? Thanks

Answer 1

[GenoMax]

See: Why do I have more reads in my .bam file than in my .fastq input file?
Samtools flagstat number of reads do not match actual total number of reads.