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SAM

96 bytes added, 11:05, 30 July 2010
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* length of this group from the leftmost position to the rightmost position, ISIZE or TLEN
* the query sequence for this alignment, SEQ
* 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[[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.
==== What is a CIGAR? ====
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.
 
==== What is QUAL? ====
 
==== What are TAGs? ====
== Example SAM ==