Has anybody seen a bimodal distribution of indels for reads with a mapping quality < 30 or has an explanation for it?
Brief background:
- Illumina paired end 90bp reads with a 500bp insert.
- file called bimodal_indels_poolseq is pooled DNA from 100 presumably unrelated individuals (not barcoded).
- file calle bimodal_indels_inbred_line is pooled DNA from at least 10, maybe 30 individuals from an inbred line (I don't recall the exact number off the top of my head).
- Mapped with BWA mem.
- Most reads (>80%) have a mapping quality >=30.
I'm not really concerned as I can set the mapping threshold at 30 without too much loss of data but I am curious to know what might be causing more indels to appear at those locations.
Brief background:
- Illumina paired end 90bp reads with a 500bp insert.
- file called bimodal_indels_poolseq is pooled DNA from 100 presumably unrelated individuals (not barcoded).
- file calle bimodal_indels_inbred_line is pooled DNA from at least 10, maybe 30 individuals from an inbred line (I don't recall the exact number off the top of my head).
- Mapped with BWA mem.
- Most reads (>80%) have a mapping quality >=30.
I'm not really concerned as I can set the mapping threshold at 30 without too much loss of data but I am curious to know what might be causing more indels to appear at those locations.