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Why does IndelRealigner change MAPQ from 70 to 80?
I have bam files aligned with novoalign, and the maximum MAPQ is 70. Sometimes IndelRealigner changes the MAPQ to 80. What does this mean, and why does this happen? I have only ever seen it happen to reads with INDELs in them.
In the following read you can see the original mapq in the MQ tag was 70, but in column 5 you can see the MAPQ is now 80.
D0GKWACXX:6:2106:03781:93121 147 1 11148317 80 73M4I24M = 11148180 -234 AATGCCTTTTATCCAATCTGTAAAAACAAATGAGAAAAGACCACTGTGAAAATATCTTCCCTTTACAAAGAGCTTCATTATTTCAGTAATTCAACTACAAA ;[email protected];FFFFHHEEEAIIGEIIIIHGDHGGBGGHDGEHF>[email protected]@@B X?:Z:EM LB:Z:UDP810_2_1 OC:Z:72M3I3M1I22M PG:Z:novoalign RG:Z:6 MQ:i:70 PQ:i:60 UQ:i:0 AS:i:60 PU:Z:120112_NIOBE_D0GKWACXX.6.1955633