Read one SAM alignment record
Interpret a simple SAM record's position, mapping quality, CIGAR operations, and pair flags.
Interpret this simplified SAM evidence: read r17 maps to chr2 at POS 1001 with MAPQ 12 and CIGAR 20M5S near a candidate breakpoint. SAM fields tell you where the read maps, how confidently it maps, and how the read sequence fits the reference. A browser pileup can look clean while the underlying record has low mapping quality, clipping, or alternative alignments that weaken the evidence. Read the position RNAME chr2 and POS 1001 place the leftmost aligned base at coordinate 1001 in SAM's 1-based coordinate convention. The coordinate only makes sense with the reference assembly and contig naming used to…
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