what does "q2" mean in bam-readcount results?

Question

[gongchangzhaojie]

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!

Answer 1

[ernfrid]

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 ( http://seqanswers.com/forums/showpost.php?p=17491&postcount=3). See the SomaticSniper paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268238/) 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.