http://samtools.sourceforge.net/SAM1.pdf
In the SAM format alignment section, the bitwise FLAG is as above table.
If the FLAG=165
OR FLAG=1133,
Then which category it falls in? Need a little explanation.
Thanks.
Code:
FLAG: bitwise FLAG. Each bit is explained in the following table: Bit Description 0x1 template having multiple segments in sequencing 0x2 each segment properly aligned according to the aligner 0x4 segment unmapped 0x8 next segment in the template unmapped 0x10 SEQ being reverse complemented 0x20 SEQ of the next segment in the template being reversed 0x40 the rst segment in the template 0x80 the last segment in the template 0x100 secondary alignment 0x200 not passing quality controls 0x400 PCR or optical duplicate
If the FLAG=165
OR FLAG=1133,
Then which category it falls in? Need a little explanation.
Thanks.
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