sam flag count

Question

[Picoskia]

Dear all,

I have paired-end data of 150bp and i use bwa-mem to align it.

bwa-mem ref_genome R1.fq.gz  R2.fq.gz > aligned_reads.sam

After the alignment, i have check the flags proportions and there is something that i do not understand, i have different count for sam flags 99/147 or 83/163.

99: 6239811
147: 6241593

 

83: 8113628
163: 8112417

This is the first time i have this, usually i get the same number of flags for 99/147 or 83/163.
Does it means that there is a problem during the alignment ?

Thank you for your help!

[GenoMax]

You can also check: https://www.samformat.info/sam-format-flag

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

Answer 1

[Buffo]

Decoding sam flags

[ Edited link (ATpoint) ]

[ATpoint]

Edited the link, please try again.

[Picoskia]

thank you for the link but the thing that i do not understand is if a have a count of for example 2000 reads for sam flag 99 i should get also the same number of reads for its mate 147?