First, you probably don't need to set the
-T flag, I believe that to be the alignment score (the sum of reward + penalties).
If the score were zero, the alignment did not really work. I don't think
-T =0 does anything. I think
-T it is more of a way to select high scoring alignments rather than low-scoring ones.
bwa won't even look for low-scoring alignments to begin with.
In general, you should aim to produce more/all alignments, then filter your BAM file later, rather than forcing the aligner to make various decisions. There is little to be gained in most cases.
The mapping quality filter is
samtools) would be a way to filter out multi mapped reads as bwa assigns a
mapQ=0 for multimapped reads.
Now as for the gaps, it is a bit curious, but what region is this, show more information, what regions is this, also download some of the SNP/annotation data they have on the website, see if anything overlaps here
the human genome took many tries to complete, the chimp has nowhere that much effort put into it.