SAM File 1-based Leftmost Mapping Position in Relation to Strand

Cited from Re: [Samtools-help] Questions about SAM format

"It's always the smaller of the two "end"-coordinates, on the positive strand (the strand that is given in your reference fasta). So, in a 100bp reference, if your 25bp read came from / is mapped to the negative strand right up against its 5'-end, the position in the SAM line would be 76. If you have another read that came from the positive strand right up against its 3'-end, the position in the SAM line would *also* be 76. Use the strand flag to distinguish between the two cases."