Eland tells me the best hit has one mismatch, but the best hit found by Maq has two mismatches. What happens?
Maq is quality-aware. Before alignment, Maq divides base qualities by 10 and then cuts off the decimal part. In alignment, hit A is said to be better than hit B if the sum of the 10-divided quality values of mismatched bases of A is smaller. Maq does not always favour the position yielding fewer mismatches. Note that dividing qualities by 10 will reduce the resolution of qualities and may lead to mapping errors for reads with low qualities. These wrongly mapped reads usually get very low mapping qualities. They are wrong anyway, which is the trade-off to make Maq faster. Furthermore, counting number of mismatches is not always the right thing, either. • I am using the default option to run `maq map’. I see hits containing a lot of mismatches. Is this a bug? No, it is not. By default, maq guarantees that all hits with up to 2 mismatches in the first 24bp can be found, and can also find part of hits with 3 or 4 mismatches in the first 24bp. There is no explicit cut off on the mismatches
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