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Table 2 Attributes of the Bio::DB::Alignment object

From: Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments

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