Q25 the edit distance equals mismatches and is

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Unformatted text preview: to a wrong alignment. •  Sensi)vity of the alignment algorithm. The true hit is more likely to be missed by an algorithm with low sensi0vity, which also causes mapping errors. •  Paired end or not. Reads mapped in pairs are more likely to be correct. BWA Specific High Scores A read alignment with a mapping quality 30 or above usually implies: –  The overall base quality of the read is good. –  The best alignment has few mismatches. –  The read has few or just one “good” hit on the reference, which means the current alignment is s0ll the best even if one or two bases are actually muta0ons or sequencing errors. BWA Specific Low Scores Surprisingly difficult to track down the exact behavior •  Q=0 if a read can be aligned equally well to mul0ple posi0ons, BWA...
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