Bismark SAM output (default)
| num |
name |
description |
| 1 |
QNAME |
- seq-ID |
| 2 |
FLAG |
- description of read |
| 3 |
RNAME |
- chromosome |
- Reference sequence NAME of the alignment |
| 4 | POS | - start position |
| 5 | MAPQ | - MAPing Quality
- only calculated for Bowtie2, always 255 for Bowtie |
| 6 | CIGAR | - CIGAR string |
| 7 | RNEXT | - Reference sequence name of the primary alignment of the NEXT read in the template |
| 8 | PNEXT | - 1-based Position of the primary alignment of the NEXT read in the template |
| 9 | TLEN | - signed observed Template LENgth |
| 10 | SEQ | - segment SEQuence |
| 11 | QUAL | - Phred33 scale |
| 12 | NM-tag | - edit distance to the reference |
| 13 | MD-tag | - base-by-base mismatches to the reference |
| 14 | XM-tag | - methylation call string |
| 15 | XR-tag | - read conversion state fore the alignment |
| 16 | XG-tag | - genome conversion state fore the alignment |
2. FLAG
6. CIGAR
- ex1.
141M
- ex2.
9M1D58M
- 9개 match or mismatch + 1개 deletion + 58개 match or mismatch
7. RNEXT