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, 11:05, 30 July 2010
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| * length of this group from the leftmost position to the rightmost position, ISIZE or TLEN | | * length of this group from the leftmost position to the rightmost position, ISIZE or TLEN |
| * the query sequence for this alignment, SEQ | | * the query sequence for this alignment, SEQ |
− | * the query quality for this alignment, QUAL, one for each base in the query sequence. | + | * the query quality for this alignment, [[SAM# What is QUAL?|QUAL]], one for each base in the query sequence. |
− | * Additional optional information is also contained within the alignment, TAGS. A bunch of different information can be stored here and they appear as key/value pairs. See the spec for a detailed list of commonly used tags and what they mean. | + | * Additional optional information is also contained within the alignment, [[SAM#What are TAGs|TAGs]]. A bunch of different information can be stored here and they appear as key/value pairs. See the spec for a detailed list of commonly used tags and what they mean. |
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| ==== What is a CIGAR? ==== | | ==== What is a CIGAR? ==== |
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| The POS indicates that the read aligns starting at position 5 on the reference. | | The POS indicates that the read aligns starting at position 5 on the reference. |
| The CIGAR says that the first 3 bases in the read sequence align with the reference. The next base in the read does not exist in the reference. Then 3 bases align with the reference. The next reference base does not exist in the read sequence, then 5 more bases align with the reference. Note that at position 14, the base in the read is different than the reference, but it still counts as an M since it aligns to that position. | | The CIGAR says that the first 3 bases in the read sequence align with the reference. The next base in the read does not exist in the reference. Then 3 bases align with the reference. The next reference base does not exist in the read sequence, then 5 more bases align with the reference. Note that at position 14, the base in the read is different than the reference, but it still counts as an M since it aligns to that position. |
| + | |
| + | ==== What is QUAL? ==== |
| + | |
| + | ==== What are TAGs? ==== |
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| == Example SAM == | | == Example SAM == |