Table 3 Attributes and methods of the Bio::DB::Pileup object
consensus | the consensus nucleotide calculated as the nucleotide with highest count multiple nucleotides returned in a tie |
coverage | the number of reads covering this position |
non_ref_count | the number of reads that disagree with the reference nucleotide |
non_ref_count_hash | a Hash with A,T,G and C as keys and the number each nucleotide appears in the pileup when that nucleotide is not |
| Â | the reference |
pos | the position in the reference sequence that this pileup represents |
read_bases | the read nucleotides covering this position |
read_quals | the quality scores of the read nucleotides covering this position |
ref_base | the reference sequence nucleotide |
ref_count | the number of times the reference nucleotide appears in the read nucleotides covering this position |
ref_name | the name of the reference sequence |
ar1, ar2, ar3 | the allele calls from pileup |
consensus1 | the consensus of the reads according to SAMtools method of calculation |
consensus_quality1 | the quality score of the consensus according to SAMtools method of calculation |
rms_mapq1 | the root mean square mapping quality at the position |
snp_quality1 | the SNP quality at the position |