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How to interpret the meaning of flag=0 in the alignment results of BAM files generated by bwa-mem2 mem #400

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wlhCNU opened this issue Sep 1, 2023 · 0 comments
Open

How to interpret the meaning of flag=0 in the alignment results of BAM files generated by bwa-mem2 mem #400

wlhCNU opened this issue Sep 1, 2023 · 0 comments

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@wlhCNU
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wlhCNU commented Sep 1, 2023

We utilized the BWA-MEM2 with the command "bwa-mem2 mem -t 16 -k 51 -T 51" to align sequences of length 51-kmer to the genome. In the resulting BAM file, we observed that in many instances, the second column had flag values of 0, while in the sixth column, there were results showing perfect matches. How to interpret the occurrence of flag=0 in this context?
Thanks.
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