sam/ bam format

sam or bam (compressed version) is used to store NGS alignment data.

QNAMEthe sequence/ read name
FLAGbitwise flag
RNAMEthe reference sequence name
POSthe position in the reference sequence (1-based indices)
MAPQthe mapping quaility
RNEXTRef. name of the mate/next read
PNEXTPosition of the mate/next read
TLENthe template length for paired-end reads
SEQthe read sequence
QUALthe base call qualities of the read sequence (same as in FASTQ format)

  1. SAMv1 specs
  2. Galaxy Wiki

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