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 |