ArrayExpress

high throughput sequence alignment protocol

The reads were mapped to the human hg19 reference genome (autosomes+X+Y+M) with the GEM mapper v 1.349 mapping entire reads, and split mapping the unmapped reads (see

for settings). In the bam files, mapping quality is scored as follows: 1) Matches which are unique, and do not have any subdominant match: 251 >= MAPQ >= 255, XT=U ; 2) Matches which are unique, and have subdominant matches but a different score: 175 >= MAPQ >= 181, XT=U ; 3) Matches which are putatively unique (not unique, but distinguishable by score): 119 >= MAPQ >= 127, XT=U ; Matches which are a perfect tie: 78 >= MAPQ >= 90, XT=R. Number of mismatches is not reflected in MAPQ but the information of total mismatches in both mates is found in the NM flag.

GEM mapper 1.349