srsilva Notas

https://broadinstitute.github.io/picard/explain-flags.html

Sam format: column information: QNAME: Query name of the read or the read pair FLAG: Bitwise flag (pairing, strand, mate strand, etc.) RNAME: Reference sequence name POS: 1-Based leftmost position of clipped alignment MAPQ: Mapping quality (Phred-scaled) CIGAR: Extended CIGAR string (operations: MIDNSHP) MRNM: Mate reference name (‘=’ if same as RNAME) MPOS: 1-based leftmost mate position ISIZE: Inferred insert size SEQQuery: Sequence on the same strand as the reference QUAL: Query quality (ASCII-33=Phred base quality) FURTHER DETAILS OF SAM FORMAT: http://samtools.sourceforge.net/SAM1.pdf