Allelic depths for the ref and alt alleles in the order listed
DP
Approximate read depth (reads with MQ=255 or with bad mates are filtered)
GQ
Genotype Quality
GT
Genotype
MQ
RMS Mapping Quality
PL
Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic
VF
Variant Frequency, the ratio of the sum of the called variant depth to the total depth
Table 4 VCF INFO Entries
Entry
Description
AC
Allele count in genotypes, for each ALT allele, in the same order as listed
AF
The allele frequency from all populations of 1000 genomes data
AN
Total number of alleles in called genotypes
DP
Approximate read depth; some reads may have been filtered
QD
Variant Confidence/Quality by Depth
BLOCKAVG_min30p3a
Non-variant site block. All sites in a block are constrained to be non-variant, have the same filter value, and have all sample values in range [x,y] , y <= max(x+3,(x*(1+0.3))). All printed site block sample values are the minimum observed in the region spanned by the block
BaseQRankSum
Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities
DS
Were any of the samples downsampled?
Dels
Fraction of Reads Containing Spanning Deletions
END
End position of the region described in this record
FS
Phred-scaled p-value using Fisher's exact test to detect strand bias
HRun
Largest Contiguous Homopolymer Run of Variant Allele In Either Direction
HaplotypeScore
Consistency of the site with at most two segregating haplotypes
MQ
RMS Mapping Quality
MQ0
Total Mapping Quality Zero Reads
MQRankSum
Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities
ReadPosRankSum
Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias
SB
Strand Bias
VQSLOD
Log odds ratio of being a true variant versus being false under the trained gaussian mixture model
culprit
The annotation that was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out
set
Source VCF for the merged record in CombineVariants