diff --git a/docs.it4i/anselm/software/omics-master/overview.md b/docs.it4i/anselm/software/omics-master/overview.md index 7a827c97b6cd5212bc932779b870e4ac8f8464cf..8d3eb3d3ea5368b1b0d09cec9ec8ca7006fbf1c4 100644 --- a/docs.it4i/anselm/software/omics-master/overview.md +++ b/docs.it4i/anselm/software/omics-master/overview.md @@ -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 â€\’ 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.