Each line consists of mapping quality threshold, #mapped reads with mapQ no less than the 1st column and #mismapped reads. It does not show #reads with mapQ=0. If we include mapQ=0 mappings, the sensitivity of bwa is also good for simulated data, but on single-end real data, the low-quality tail on reads makes bwa much worse. This is what Steven and Ben have observed. This is also why it is recommended to enable trimming when using bwa.
BWA always gives mapQ 0 to repetitive hits, but other mappers (gsnap, bowtie2 and novoalign) may give mapQ<=3 to repetitive hits. This is theoretically correct. I may further set a mapQ threshold 1-4 when plotting.
BWA always gives mapQ 0 to repetitive hits, but other mappers (gsnap, bowtie2 and novoalign) may give mapQ<=3 to repetitive hits. This is theoretically correct. I may further set a mapQ threshold 1-4 when plotting.
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