gistfile1.txt

Number of samples with datag
Total read depth at the locusg
Total read depth per bp at the locus; bases in reads overlapping / bases in haplotypeg
Total number of alternate alleles in called genotypesg
Total number of alleles in called genotypesg
Estimated allele frequency in the range (0,1]g
Reference allele observation count, with partial observations recorded fractionallyg
Alternate allele observations, with partial observations recorded fractionallyg
Reference allele observation count, with partial observations recorded fractionallyg
Alternate allele observations, with partial observations recorded fractionallyg
Reference allele quality sum in phredg
Alternate allele quality sum in phredg
Reference allele quality sum in phred for partial observationsg
Alternate allele quality sum in phred for partial observationsg
Number of reference observations on the forward strandg
Number of reference observations on the reverse strandg
Number of alternate observations on the forward strandg
Number of alternate observations on the reverse strandg
Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequalityg
Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequalityg
Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygousg
Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequalityg
Run length: the number of consecutive repeats of the alternate allele in the reference genomeg
Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequalityg
Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequalityg
Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate alleleg
Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate alleleg
End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequalityg
End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequalityg
Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.g
The log odds ratio of the best genotype combination to the second-best.g
Number of genotyping iterations required to reach convergence or bailout.g
The type of allele, either snp, mnp, ins, del, or complex.g
The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.g
Number of unique non-reference alleles in called genotypes at this position.g
Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.g
allele lengthg
Mean mapping quality of observed alternate allelesg
Mean mapping quality of observed reference allelesg
Proportion of observed alternate alleles which are supported by properly paired read fragmentsg
Proportion of observed reference alleles which are supported by properly paired read fragmentsg
Fraction of observations supporting the alternate observed in reads from ILLUMINAg
Genotypeg
Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotypeg
Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidyg
Read Depthg
Reference allele observation countg
Sum of quality of the reference observationsg
Alternate allele observation countg
Sum of quality of the alternate observationsg