SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Further information about it can be read in the SAM format specifications document.
The following example shows a valid mapped read-pair in SAM format:
ID:1:2:3 129 11 127926 1 75M = 128047 122 CTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCG @@@FFFFFHDHFFGGIIGHGIIJIIIFGFEEFHECDHGCBHIGIIDCACA(;5?@?ED@;?;C?688;?(82::>? ID:1:2:3 65 11 128047 1 75M = 127926 -12 CCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCACATTGCCCAGCTGTTC @@@FFADFGHHHHGIGHGCGGIIIGGHCHHIJJJIJIGD?FDGHIGHIIIIJAHGHHHGFD?DECCCCE?DCC>@C
Multiple alignments:
ID:1:2:3 385 1 135712 1 76M = 135833 122 CTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCG @@@FFFFFHDHFFGGIIGHGIIJIIIFGFEEFHECDHGCBHIGIIDCACA(;5?@?ED@;?;C?688;?(82::>? ID:1:2:3 321 1 135833 1 76M = 135712 -12 CCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCACATTGCCCAGCTGTTC @@@FFADFGHHHHGIGHGCGGIIIGGHCHHIJJJIJIGD?FDGHIGHIIIIJAHGHHHGFD?DECCCCE?DCC>@C ID:1:2:3 385 1 662078 1 76M = 662199 122 CTACCAGGGCCGCTGGGAGCTGGGCAGGAGCTGAGTCCAAAGACGTTGTTGGGACCTGGAGTCGGGCCAGAGTCCG @@@FFFFFHDHFFGGIIGHGIIJIIIFGFEEFHECDHGCBHIGIIDCACA(;5?@?ED@;?;C?688;?(82::>? ID:1:2:3 321 1 662199 1 76M = 662078 -12 CCGGGAGGCTGCAAGTGGGTCTGAGAGGCCAACTTGAGGAGGCCTGGCCTCTGCCTCCCACATTGCCCAGCTGTTC @@@FFADFGHHHHGIGHGCGGIIIGGHCHHIJJJIJIGD?FDGHIGHIIIIJAHGHHHGFD?DECCCCE?DCC>@C
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