Used bowtie2 2.2.6. I have the following 2 alignments, with exactly the same CIGAR. The only difference is that there is a mismatch in the second alignment. My scoring options are: --rdg 2,1 --rfg 2,1 --score-min L,18,0 --np 1 --ma 1 --mp 5,1.

For the first alignment AS = 21 (M) - 2 (XO:i:1) - 15 (XG:i:15) + 22 (M) = 26, which matches.

For the second alignment AS = 21 (M) - 2 (XO:i:1) - 15 (XG:i:15) + 21 (M) - 5 (XM:i:1) = 20, which is diffrent from AS.i:24 in the alignment. Is there something I'm missing?

Alignment 1: tag_344761|1 0 MI0000167_mmu-mir-142a 4 255 6S21M15D22M * 0 0 CTTTCTCATAAAGTAGAAAGCACTACTTGTAGTGTTTCCTACTTTATGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:26 XN:i:0 XM:i:0 XO:i:1 XG:i:15 NM:i:15 MD:Z:21^AACAGCACTGGAGGG22 YT:Z:UU Alignment 2: tag_457953|1 0 MI0000167_mmu-mir-142a 4 255 6S21M15D22M * 0 0 GTCTCTCATAAAGTAGAAAGCACTACTTGTAGTGTTNCCTACTTTATGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:24 XN:i:0 XM:i:1 XO:i:1 XG:i:15 NM:i:16 MD:Z:21^AACAGCACTGGAGGG9T12 YT:Z:UU