Each Alignment has:
* query name, QNAME (SAM)/read_name (BAM). It is used to group/identify alignments that are together, like paired alignments or a read that appears in multiple alignments.
Not all alignments contain The rest of the alignment fields may be set to default values if the information is unknown.
* leftmost position of where the next alignment in this group maps to the reference, MPOS or PNEXT. For SAM, the reference starts at 1, so this value is 1-based, while for BAM the reference starts at 0,so this value is 0-based. Beware to always use the correct base when referencing positions.
* length of this group from the leftmost position to the rightmost position, ISIZE or TLEN
* the sequence for this alignment, SEQ* the quality for this alignment, QUAL
* 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.
== Example SAM ==