3 If converting GFF3 to SAM, store any key, values from column 9 in the CT tag, except for the unique

ID which is used for the QNAME. GFF3 columns 1 (seqid), 4 (start) and 5 (end) are encoded using SAM columns RNAME, POS and CIGAR to hold the length. GFF3 columns 3 (type) and 7 (strand) are stored explicitly in the CT tag. Remaining GFF3 columns 2 (source), 6 (score), and 8 (phase) are stored in the CT tag using key values FSource, FScore and FPhase (uppercase keys are restricted in GFF3, so these names avoid clashes). Split location features are described with multiple lines in GFF3, and similarly become multi-segment dummy reads in SAM, with the RNEXT and PNEXT columns lled in appropriately. In the absence of a convention in SAM/BAM for reads wrapping the origin of a circular genome, any GFF3 feature line wrapping the origin must be split into two segments in SAM.