Skip to content
Snippets Groups Projects
Commit ab77b1a2 authored by Pavel Jirásek's avatar Pavel Jirásek
Browse files

Merge branch 'content_revision' into 'master'

Content revision

See merge request !92
parents 3650e1bd 5fe32692
No related branches found
No related tags found
5 merge requests!368Update prace.md to document the change from qprace to qprod as the default...,!367Update prace.md to document the change from qprace to qprod as the default...,!366Update prace.md to document the change from qprace to qprod as the default...,!323extended-acls-storage-section,!92Content revision
Pipeline #
......@@ -63,19 +63,19 @@ The SAM format (1) consists of one header section and one alignment section. The
In SAM, each alignment line has 11 mandatory fields and a variable number of optional fields. The mandatory fields are briefly described in Table 1. They must be present but their value can be a ‘\’ or a zero (depending on the field) if the
corresponding information is unavailable.
| No. | Name | Description |
| No. | Name | Description |
| --------- | ---------- | ----------------------------------------------------- |
| 1 | QNAME | Query NAME of the read or the read pai |
| 2 | FLAG | Bitwise FLAG (pairing,strand,mate strand,etc.) |
| 3 | RNAME | <p>Reference sequence NAME |
| 4 | POS | <p>1-Based leftmost POSition of clipped alignment |
| 5 | MAPQ | <p>MAPping Quality (Phred-scaled) |
| 6 | CIGAR | <p>Extended CIGAR string (operations:MIDNSHP) |
| 7 | MRNM | <p>Mate REference NaMe ('=' if same RNAME) |
| 8 | MPOS | <p>1-Based leftmost Mate POSition |
| 9 | ISIZE | <p>Inferred Insert SIZE |
| 10 | SEQ | <p>Query SEQuence on the same strand as the reference |
| 11 | QUAL | <p>Query QUALity (ASCII-33=Phred base quality) |
| 3 | RNAME | Reference sequence NAME |
| 4 | POS | 1-Based leftmost POSition of clipped alignment |
| 5 | MAPQ | MAPping Quality (Phred-scaled) |
| 6 | CIGAR | Extended CIGAR string (operations:MIDNSHP) |
| 7 | MRNM | Mate REference NaMe ('=' if same RNAME) |
| 8 | MPOS | 1-Based leftmost Mate POSition |
| 9 | ISIZE | Inferred Insert SIZE |
| 10 | SEQ | Query SEQuence on the same strand as the reference |
| 11 | QUAL | Query QUALity (ASCII-33=Phred base quality) |
Table 1 . Mandatory fields in the SAM format.
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment