MAPQ Scoring

By default, the MAPQ calculation for RNA-Seq is identical to DNA-Seq. The primary contributor to MAPQ calculation is the difference between the best and second-best alignment scores. Therefore, adjusting the alignment scoring parameters impacts the MAPQ estimate. These adjustments are outlined in Smith-Waterman Alignment Scoring Settings .

The --mapq-strict-sjs option is specific to RNA, and applies where at least one exon segment is aligned confidently, but there is ambiguity regarding possible splice junctions. When this option is set to 0, a higher MAPQ value is returned, expressing confidence that the alignment is at least partially correct. When this option is set to 1, a lower MAPQ value is returned, reflecting the splice junction ambiguity.

Some downstream tools, such as Cufflinks, expect the MAPQ value to be a unique value for all uniquely mapped reads. This value is specified with the --rna-mapq-unique option. Setting this option to a nonzero value overrides all MAPQ estimates based on alignment score. Instead, all uniquely mapped reads have a MAPQ set to the value of --rna-mapq-unique. All multimapped reads have a MAPQ value of int(-10*log10(1 ‑ 1/NH), where the NH value is the number of hits (primary and secondary alignments) for that read.