ReadCounts Output

A tab-separated values file consisting of the computed read-counts. This file contains the read counts for each SNV locus in each read group (by default, each BAM file):

CHROM

Chromosome identifier

POS

Chromosome position of the variant

REF

Reference allele nucleotide

ALT

Variant allele nucleotide

ReadGroup

Name of the aligned reads file for the following read counts.

SNPCountForward

Number of forward oriented variant reads in the paired end alignment.

SNPCountReverse

Number of reverse oriented variant reads in the paired end alignment.

RefCountForward

Number of forward oriented reference reads in the paired end alignment.

RefCountReverse

Number of reverse oriented reference reads in the paired end alignment.

SNPCount

Total number of variant reads.

RefCount

Total number of reference reads.

GoodReads

Total number of reads considered.

%BadReads

Proportion of reads not counted.

VAF

Proportion of variant reads.

Extended Output Columns

Genotype Likelihood

HomoVarSc

Score of locus as homozygous variant.

HetSc

Score of locus as heterozygous reference and variant.

HomoRefSc

Score of locus as homozygous reference.

VarDomSc

Score of locus as dominant for the variant allele.

RefDomSc

Score of locus as dominant for the reference allele.

NotHomoVarpV

p-Value of read counts with respect to homozygous variant null model.

NotHomoRefpV

p-Value of read counts with respect to homozygous reference null model.

NotHetpV

p-Value of read counts with respect to heterozygous reference and variant null model.

VarDompV

p-Value of increased variant read counts with respect to heterozygous reference and variant null model.

RefDompV

p-Value of increased reference read counts with respect to heterozygous reference and variant null model.

NotHomoVarFDR

Multiple-test corrected FDR significance of read counts with respect to homozygous variant null model.

NotHomoRefFDR

Multiple-test corrected FDR significance of read counts with respect to homozygous reference null model.

NotHetFDR

Multiple-test corrected FDR significance of read counts with respect to heterozygous reference and variant null model.

VarDomFDR

Multiple-test corrected FDR significance of increased variant read counts with respect to heterozygous reference and variant null model.

RefDomFDR

Multiple-test corrected FDR significance of increased reference read counts with respect to heterozygous reference and variant null model.

Read filtering statistics

OtherCountForward

Reads with unexpected nucleotides in the forward oriented aligned read.

OtherCountReverse    

Reads with unexpected nucleotides in the reverse oriented aligned read.

OtherCount 

Reads with unexpected nucleotides.

FilteredSNVLociReads

Total number of reads that passed the read-filters.

SNVLociReads   

Total number of reads covering the site.

Alignment:IsDuplicate

Alignment has the duplicate flag.

Alignment:IsQCFail     

Alignment has the QCFail flag.

Alignment:IsSecondary  

Alignment has the secondary flag.

Alignment:IsUnmapped   

Alignment has the unmapped flag.

BadCIGAROperation

Unexpected CIGAR string operation.

BaseQualityTooLow

Base quality at locus is too low.

DuplicateRead

Duplicate read.

GapInQueryAtSNVLocus

Gap in the alignment at the site of interest.

MappingQualityTooLow

Mapping quality too low.

MultipleAlignments

Read aligns to more than one region.

OrphanRead

Read’s mate pair is unmapped.

OverlapRead

Paired-end read covers the site of iterest redundantly.

QueryIndelAtSNVLocus   

Indel in the read at the site of interest.

SNVLocusAtEndOfRead

Site of interest is too close to the start or end of the read.

SubstitutionNearSNVLocus       

Site of interest is too close to another substitution.

TooManyEdits

Read alignment requires too many edits.

TooManyEditsOtherThanSNV

Read alignment requires too many edits other than at the site of interest.

TooManyQueryGaps

Read is aligned using too many gaps.

TooShort

Read is too short.