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 |
| |
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 |
1ten column format only.