Sample ID Genotypes of Interest
The DNA + RNA Amplicon app creates a VCF file (*.sampleID.vcf) and a CSV file (*.sampleID.csv). Each row in the output files represent a variant call of interest. The fields of the CSV file are defined in the following table.
|
Statistic |
Definition |
|---|---|
|
Chr |
Name of the reference chromosome. |
|
Position |
Position within the reference chromosome. |
|
ID |
The identifier in dbSNP |
|
RefAllele |
The reference allele |
|
AltAllele |
The alt allele |
|
Filters |
The filters that have been applied to the variant. |
|
GT |
The genotype of the variant following the standard vcf annotation (eg, 0/0, 0/1, 1/1, 2/2, ./.). |
|
GenotypeText |
Human readable genotype of the variant: REF (reference), HET (heterozygous), HOM (homozygous alternate), NO_CALL, FORCED_REPORT, or OTHER_CALL. |
|
GenotypeForwardAlleles |
The observed alleles on the forward strands, separated by "/". For example: Ref/Ref, Ref/Alt, Alt/Alt, or NA for no call. |
|
GenotypeTopAlleles |
The two single nucleotide alleles on the top strands, concatenated (eg, AT). When TopBotStrand is TOP, GenotypeTopAlleles contains bases in GenotypeForwardAlleles ordered alphabetically; When TopBotStrand is BOT, GenotypeTopAlleles contains complements of the base ordered alphabetically; When TopBotStrand is NA, GenotypeTopAlleles is NA. |
|
TopBotStrand |
Top or bottom strand (ie, TOP, BOT, or NA for indels). See the table below for the strand designation. |
|
Allele1Top |
The first (top) allele in the allele pair GenotypeTopAlleles (A/T/G/C or NA for indels). |
|
Allele2Top |
The second (top) allele in the allele pair GenotypeTopAlleles (A/T/G/C or NA for indels). |
|
VariantQuality |
Phred-scaled quality score indicating how confident we are in this asserted haplotype. |
|
GQ |
Phred-scaled quality score indicating how confident we are in this asserted genotype. |
|
AD |
The number of reads containing the variant allele. |
|
DP |
The number of reads aligned at this position. |
|
VF |
The proportion of the variant allele among all alleles being considered. |
|
GoIFileName |
The name of the input genotypes of interest (GoI) VCF files. If multiple GoI files contain the same variant, the first GoI file name is used. |