Table 2.

Attributes of the Bio::DB::Alignment object

calend	nucleotide position of the end of the alignment
cigar	CIGAR string describing the matches/mismatches
failed_quality	this read failed the quality threshold
first_in_pair	first of a pair
is_duplicate	this read is a suspected optical or PCR duplicate
is_mapped	the read was aligned
is_paired	the read is one of a pair
isize	the insert size distance between mapped mates
mapq	the PHRED scaled mapping quality of the alignment
mate_strand	the strand of the mate
mate_unmapped	the mate is unmapped
mpos	start position of the mate on the reference
pos	start position of the alignments
primary	is a primary alignment
qlen	read length
qname	read name
qual	read quality string
query_strand	strand of alignment
query_unmapped	query is unmapped
rname	name of reference to which read mapped
second_in_pair	this is second in the pair
seq	read sequence
tags	Bio::DB::Tag object representing the tags for this alignment