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docs.it4i/anselm/software/omics-master/overview.md
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@@ -63,19 +63,19 @@ The SAM format (1) consists of one header section and one alignment section. The
@@ -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
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.
corresponding information is unavailable.
| No. | Name | Description |
| No. | Name | Description |
| --------- | ---------- | ----------------------------------------------------- |
| --------- | ---------- | ----------------------------------------------------- |
| 1 | QNAME | Query NAME of the read or the read pai |
| 1 | QNAME | Query NAME of the read or the read pai |
| 2 | FLAG | Bitwise FLAG (pairing,strand,mate strand,etc.) |
| 2 | FLAG | Bitwise FLAG (pairing,strand,mate strand,etc.) |
| 3 | RNAME | <p>Reference sequence NAME |
| 3 | RNAME | Reference sequence NAME |
| 4 | POS | <p>1-Based leftmost POSition of clipped alignment |
| 4 | POS | 1-Based leftmost POSition of clipped alignment |
| 5 | MAPQ | <p>MAPping Quality (Phred-scaled) |
| 5 | MAPQ | MAPping Quality (Phred-scaled) |
| 6 | CIGAR | <p>Extended CIGAR string (operations:MIDNSHP) |
| 6 | CIGAR | Extended CIGAR string (operations:MIDNSHP) |
| 7 | MRNM | <p>Mate REference NaMe ('=' if same RNAME) |
| 7 | MRNM | Mate REference NaMe ('=' if same RNAME) |
| 8 | MPOS | <p>1-Based leftmost Mate POSition |
| 8 | MPOS | 1-Based leftmost Mate POSition |
| 9 | ISIZE | <p>Inferred Insert SIZE |
| 9 | ISIZE | Inferred Insert SIZE |
| 10 | SEQ | <p>Query SEQuence on the same strand as the reference |
| 10 | SEQ | Query SEQuence on the same strand as the reference |
| 11 | QUAL | <p>Query QUALity (ASCII-33=Phred base quality) |
| 11 | QUAL | Query QUALity (ASCII-33=Phred base quality) |
Table 1 . Mandatory fields in the SAM format.
Table 1 . Mandatory fields in the SAM format.