Commit 9b6df059 authored by Denis Jacob Machado's avatar Denis Jacob Machado

Update README.md

parent 4ee274a4
......@@ -101,29 +101,4 @@ directory as the 3 awa scripts.
Machado D.J., Janies D., Brouwer C. R., & Grant T.(under
review). Four New Complete Mitochondrial Genomes of Frogs
and a New Strategy to Infer Circularity. _Ecology and
Evolution_ (submitted Sep. 9, 2017).
# APPENDIX
## The SAM Format -- Mandatory Fields in the alignment section
SAM stands for Sequence Alignment/Map format. It is a TAB-delimited text format
consisting of a header section, which is optional, and an alignment section. If
present, the header must be prior to the alignments. Header lines start with
"@", while alignment lines do not. Each alignment line has 11 mandatory fields
for essential alignment information such as mapping position, and variable
number of optional fields for exible or aligner specific information.
| # | Field | Type | Description |
|---|-------|------|-------------|
| 1 | QNAME |String | Brief description |
| 2 | FLAG |Int | Query template NAME |
| 3 | RNAME |String | bitwise FLAG |
| 4 | POS |Int | Reference sequence NAME |
| 5 | MAPQ |Int | 1-based leftmost mapping POSition MAPping Quality |
| 6 | CIGAR |String | CIGAR string |
| 7 | RNEXT |String | Ref. name of the mate/next read |
| 8 | PNEXT |Int | Position of the mate/next read |
| 9 | TLEN |Int | observed Template LENgth |
| 10 | SEQ |String | segment SEQuence |
| 11 | QUAL |String | ASCII of Phred-scaled base QUALity+33 |
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Evolution_ (submitted Sep. 9, 2017).
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