BWA MEM question

[Liy]

Dear all,

I just have a question about bwa mem alignment. I ran the following simple command:

bwa mem <fa> <fastq> -t 5

Before the alignment I checked the number of reads with fastqc and then after alignment I counted the IDs present in the sam file with grep '<common ID> | wc -l and I got different results.
What causes the difference? Is the multi-mapper reads present in the sam file?

Total reads: 24 961 320
Aligned reads: 24 961 535

Thank you for the answere,
Regards,
Liy

[sarvidsson]

Run

samtools view -S -f 0x100 <file.sam>

to get the multimappers.