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id String | The variant ID |
names List<String> | Other names used for this genomic variation |
chromosome String | Chromosome where the genomic variation occurred |
start int | Normalized position where the genomic variation starts |
end int | Normalized position where the genomic variation ends |
reference String | Reference allele |
alternate String | Alternate allele |
length int | Length of the genomic variation, which depends on the variation type |
type VariantType | Type of variation: single nucleotide, indel or structural variation. SNV | SO:0001483 | SNP | SO:0000694 | MNV | SO:0002007 | MNP | SO:0001013 | INDEL | SO:1000032 | INSERTION | SO:0000667 | DELETION | SO:0000159 | TRANSLOCATION | SO:0000199 | INVERSION | SO:1000036 | CNV | SO:0001019 | DUPLICATION | SO:1000035 | BREAKEND |
| SYMBOLIC |
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strand String | Reference strand for this variant |
sv StructuralVariation | Information regarding Structural Variants ciStartLeft int | Confidence interval around START for imprecise variants - left | ciStartRight int | Confidence interval around START for imprecise variants - right
| ciEndLeft int | Confidence interval around END for imprecise variants - left
| ciEndRight int | Confidence interval around END for imprecise variants - right
| copyNumber int | Number of copies for CNV variants | leftSvInsSeq String | Left inserted sequence for long INSERTIONS | rightSvInsSeq String | Rightinserted sequence for long INSERTIONS | type StructuralVariantType | Structural variation type COPY_NUMBER_GAIN | SO:0001742 | COPY_NUMBER_LOSS | SO:0001743 | TANDEM_DUPLICATION | SO:1000173 |
| breakend Breakend | mate BreakendMate | chromosome |
| position |
| ciPositionLeft | Confidence interval arount BREAKEND position - left | ciPositionRight | Confidence interval arount BREAKEND position - right |
| orientation BreakendOrientation | SE | Start - End t[p[ piece extending to the right of p is joined after t | SS | Start - Start t]p] reverse comp piece extending left of p is joined after t | ES | End - Start ]p]t piece extending to the left of p is joined before t | EE | End - End [p[t reverse comp piece extending right of p is joined before t |
| insSeq String | Sequence inserted between the two breakends |
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studies List<StudyEntry> | Information specific to each study the variant was read from, such as samples or statistics studyId String | Unique identifier of the study | secondaryAlternates List<AlternateCoordinate> | Alternate alleles that appear along with a variant alternate chromosome String | Chromosome where the genomic variation occurred | start int | First position 1-based of the alternate | end int | End position 1-based of the alternate | reference String | Reference allele | alternate String | Alternate allele | type VariantType | Type of variation: single nucleotide, indel or structural variation |
| files List<FileEntry> | List of files from the study where the variant was present fileId String | Unique identifier of the source file | call OriginalCall |
variantId | Original call position for the variant, if the file was normalised. | alleleIndex | Alternate allele index of the original multi-allellic variant call in which was decomposed |
| data Map<String, String> | File related data that depend on the format of the file the variant was initially read from. |
| sampleDataKeys List<String> | Data keys for each sample data | samples List<SampleEntry> | Genotypes and other sample-related information. Each position is related with one sample. The content are lists of values in the same order than the sampleDataKeys array. The length of this lists must be the same as the sampleDataKeys field. sampleId String | Unique sample identifier | fileIndex int | Relative position of the file within the StudyEntry | data List<String> | Sample data |
| stats List<VariantStats> | Statistics of the genomic variation, such as its alleles/genotypeCounters count or its minimum allele frequency, grouped by cohort id. cohortId String | Cohort identifier | alleleCount int | Total number of alleles in called genotypeCounters. Does not include missing alleles | refAlleleCount int | Number of reference alleles found in this variant | altAlleleCount int | Number of main alternate alleles found in this variants. Does not include secondary alternates | refAlleleFreq float
| Reference allele frequency calculated from refAlleleCount and alleleCount, in the range (0,1) | 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 missing genotypeCounters | genotypeCount Map<int> | Count for each genotype found | genotypeFreq Map<float> | Genotype frequency for each genotype found | filterCount Map<int> | Number of samples with non-missing genotype with that specific filter | filterFreq Map<float> | Frequency of each filter. Count divided by the number of non-missing samples | qualityAvg float | The weighted average of the Quality, computed only for non-missing samples | maf float | Minor allele frequency | mgf float | Minor genotype frequency | mafAllele string | Allele with minor frequency | mgfGenotype string | Genotype with minor frequency |
| scores List<VariantScore> | id | Variant score ID | cohort1 | Main cohort used for calculating the score | cohort2 | Optional secondary cohort used for calculating the score | score | Score value | pValue | Score p value |
| issues List<IssueType> | type IssueType | DUPLICATION |
| DISCREPANCY |
| MENDELIAN_ERROR |
| DE_NOVO |
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| sample SampleEntry |
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annotation |
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