cohortId String | Unique cohort identifier within the study. |
sampleCount int | Count of samples with non-missing genotypes in this variant from the cohort. This value is used as denominator for genotypeFreq. |
fileCount int | Count of files with samples from the cohort that reported this variant. This value is used as denominator for filterFreq. |
alleleCount int | Total number of alleles in called genotypeCounters. It does not include missing alleles. This value is used as denominator for refAlleleFreq and altAlleleFreq. |
refAlleleCount int | Number of reference alleles found in this variant. |
refAlleleFreq float | Reference allele frequency calculated from refAlleleCount and alleleCount, in the range [0,1] |
altAlleleCount int | Number of main alternate alleles found in this variants. It does not include secondary alternates. |
altAlleleFreq float | Alternate allele frequency calculated from altAlleleCount and alleleCount, in the range [0,1] |
missingAlleleCount int | Number of missing alleles. |
missingGenotypeCount int | Number of genotypes with all alleles missing (e.g. ./.). It does not count partially missing genotypes like "./0" or "./1". |
genotypeCount Map<String, int> | Number of occurrences for each genotype. This does not include genotype with all alleles missing (e.g. ./.), but it includes partially missing genotypes like "./0" or "./1". Total sum of counts should be equal to the count of samples. |
genotypeFreq Map<String, float> | Genotype frequency for each genotype found calculated from the genotypeCount and samplesCount, in the range [0,1] |
maf float | Minor allele frequency. Frequency of the less common allele between the reference and the main alternate alleles. This value does not take into acconunt secondary alternates. |
mafAllele String | Allele with minor frequency. |
mgf float | Minor genotype frequency. Frequency of the less common genotype seen in this variant. This value takes into account all values from the genotypeFreq map. |
mgfGenotype String | Genotype with minor frequency. |
filterCount Map<String, int> | The number of occurrences for each FILTER value in files from samples in this cohort reporting this variant. As each file can contain more than one filter value (usually separated by ';'), the total sum of counts could be greater than to the count of files. |
filterFreq Map<String, float> | Frequency of each filter calculated from the filterCount and filesCount, in the range [0,1] |
qualityCount int | The number of files from samples in this cohort reporting this variant with valid QUAL values. This value is used as denominator to obtain the qualityAvg |
qualityAvg float | The average Quality value for files with valid QUAL values from samples in this cohort reporting this variant. Some files may not have defined the QUAL value, so the sampling could be less than the filesCount. |