I have mapped some Illumina reads onto my reference genome using Bowtie2. I only specified --nounal and left all other parameters at default.
111247311 reads; of these:
111247311 (100.00%) were paired; of these:
19249548 (17.30%) aligned concordantly 0 times
81185571 (72.98%) aligned concordantly exactly 1 time
10812192 (9.72%) aligned concordantly >1 times
I wish to extract the 81185571 reads that aligned concordantly 1 time.
I can extract concordant reads with samtools view -f 0x2, but I wonder how Bowtie2 defines reads that map concordantly exactly 1 time?
Can I extract these using the absence of XS:i or is it based on a MAPQ score threshold?