BBMap : NH:i:1 and XT:A:R

Question

[Nicolas Rosewick]

Hi,

I aligned some paired-end reads on hg19 and found some strange stuff (at least for me..). Some reads have NH:i:1 i.e. the read aligned in one position and XT:A:R i.e. XT:A:R flag indicates that the second read is repetitive. I don't understand how reads that align to one position (NH:i:1) can be repetive .. or maybe I'm missing something ?

Here's an example for a pair of reads :

M00991:78:000000000-AP8FW:1:1101:3646:9757 1:N:0:59 99  chr11   7381659 3   83M =   7381659 83  TAAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACTCATGAGCATGGAATGTTCTTCCATTTGTTTGT HHHHHHHHGHHHGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHHHHHGHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHH XT:A:R  NM:i:0  AM:i:3  NH:i:1
M00991:78:000000000-AP8FW:1:1101:3646:9757 1:N:0:59 147 chr11   7381659 3   83M =   7381659 -83 TAAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACTCATGAGCATGGAATGTTCTTCCATTTGTTTGT HHHHHHGGHHHHHHHHHHHHHHHHGHHGHHHGHHHHHHHHHGHGHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHH XT:A:R  NM:i:0  AM:i:3  NH:i

[Brian Bushnell]

NH is the number of reported alignments, not possible alignments. So it will never be greater than 1 unless you are reporting secondary alignments.

[ayaosama2111]

Could you please explain the difference between reported alignment and possible alignment?

Many thanks!

[GenoMax]

Tagging: Brian Bushnell