Question: what does "q2" mean in bam-readcount results?
gravatar for gongchangzhaojie
3.8 years ago by
gongchangzhaojie10 wrote:

I found bam-readcount to be very useful for further filtering SNVs and Indels.

However, I do not understand a few fields of bam-readcount outputs and cannot find any other information regarding some of the fields other than the github page of bam-readcount.

(1) num_q2_containing_reads → number of reads with q2 runs at the 3’ end (2) avg_distance_to_q2_start_in_q2_reads → average distance of position (as fraction of unclipped read length) to the start of the q2 run

Does anyone know what the two fields listed above mean (from bam-readcount)? What does "q2" mean?

Thank you!

sequencing snp next-gen sequence • 1.1k views
ADD COMMENTlink modified 3.7 years ago by ernfrid210 • written 3.8 years ago by gongchangzhaojie10
gravatar for ernfrid
3.7 years ago by
United States
ernfrid210 wrote:

q2 in this case means bases with Phred quality score of 2. At the time bam-readcount was written, bases of this quality indicated an error in the read as determined by Illumina's software ( See the SomaticSniper paper ( for a bit more information about why this was included. (section 3.4.2). I haven't looked to see if this is still applicable to more recent data from newer Illumina software and machines.

ADD COMMENTlink written 3.7 years ago by ernfrid210
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