|
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
|
