Spreadsheet: 2a7c8b2a-d55e-4b63-aec1-2dce68776de4
Sheet: Variants Table

The Variants table
Documentation also available at: http://gemini.readthedocs.org/en/latest/content/database_schema.html#the-variants-table
 |  | COLUMN NAME | COLUMN TYPE | [NAME]
Core VCF Fields |  | chrom | STRING | The chromosome on which the variant resides
 |  | start | INTEGER | The 0-based start position.
 |  | end | INTEGER | The 1-based end position.
 |  | variant_id | INTEGER | PRIMARY_KEY
 |  | anno_id | INTEGER | Variant transcript number for the most severely affected transcript
 |  | ref | STRING | Reference allele
 |  | alt | STRING | Alternate alele for the variant
 |  | qual | INTEGER | Quality score for the assertion made in ALT
 |  | filter | STRING | A string of filters passed/failed in variant calling
[NAME] and population genetics info |  | type | STRING | The type of variant.
 |  |  |  | Any of: [snp, indel]
 |  | sub_type | STRING | The variant sub-type.
 |  |  |  | If type is snp: [ts, (transition), tv (transversion)]
 |  |  |  | If type is indel: [ins, (insertion), del (deletion)]
 |  | call_rate | FLOAT | The fraction of samples with a valid genotype
 |  | num_hom_ref | INTEGER | The total number of of homozygotes for the reference (ref) allele
 |  | num_het | INTEGER | The total number of heterozygotes observed.
 |  | num_hom_alt | INTEGER | The total number of homozygotes for the reference (alt) allele
 |  | num_unknown | INTEGER | The total number of of unknown genotypes
 |  | aaf | FLOAT | The observed allele frequency for the alternate allele
 |  | [NAME] | FLOAT | The [NAME] probability of deviation from HWE (assumes random mating)
 |  | inbreeding_coeff | FLOAT | The inbreeding co-efficient that expresses the likelihood of effects due to inbreeding
 |  | pi | FLOAT | The computed nucleotide diversity (pi) for the site
[NAME]. |  | gts | [NAME] | A compressed binary vector of sample genotypes (e.g., “A/A”, “A|G”, “G/G”) Extracted from the VCF "GT" tag
 |  | gt_types | [NAME] | A compressed binary vector of numeric genotype “types” (e.g., 0, 1, 2) Inferred from the VCF "GT" tag
 |  | gt_phases | [NAME] | A compressed binary vector of sample genotype phases (e.g., False, True, False) Inferred from the VCF GT genotype tag’s allele delimiter:     e.g., A/G means an unphased genotype. Value is FALSE.     e.g., A|G means a phased genotype. Value is TRUE.
 |  | gt_depths | [NAME] | A compressed binary vector of the depth of aligned sequence observed for each sample Extracted from the VCF DP genotype tag.
 |  | gt_ref_depths | [NAME] | A compressed binary vector of the depth of reference alleles observed for each sample Extracted from the VCF AD genotype tag.
 |  | gt_alt_depths | [NAME] | A compressed binary vector of the depth of alternate alleles observed for each sample Extracted from the VCF AD genotype tag.
 |  | gt_quals | [NAME] | A compressed binary vector of the genotype quality (PHRED scale) estimates for each sample Extracted from the VCF GQ genotype tag.
Gene Information |  | gene | STRING | Corresponding gene name of the highly affected transcript
 |  | transcript | STRING | The variant transcript that was most severely affected
 |  |  |  | (for two equally affected transcripts, either the first one is selected (VEP) or protein_coding biotype considered (snpEff).
 |  | is_exonic | BOOL | Does the variant affect an exon for >= 1transcript?
 |  | is_coding | BOOL | Does the variant fall in a coding region (excl. 3’ & 5’ UTRs) for >= 1 transcript?
 |  | is_lof | BOOL | Based on the value of the impact col, is the variant [NAME] for >= transcript?
 |  | exon | STRING | Exon information for the severely affected transcript
 |  | codon_change | STRING | What is the codon change?
 |  | aa_change | STRING | What is the amino acid change (for an snp)?
 |  | aa_length | STRING | The length of CDS in terms of number of amino acids (only snpEff)
 |  | biotype | STRING | The ‘type’ of the severely affected transcript (e.g.protein-coding, pseudogene, rRNA etc.) (only snpEff)
 |  | impact | STRING | The consequence of the most severely affected transcript
 |  | impact_severity | STRING | Severity of the highest order observed for the variant
 |  | polyphen_pred | STRING | Polyphen predictions for the snps for the severely affected transcript (only VEP)
 |  | polyphen_score | FLOAT | Polyphen scores for the severely affected transcript (only VEP)
 |  | sift_pred | STRING | SIFT predictions for the snp’s (VEP only) for the most severely affected transcript (only VEP)
 |  | sift_score | FLOAT | SIFT scores for the predictions (only VEP)
 |  | pfam_domain | STRING | Pfam protein domain that the variant affects
Optional VCF INFO fields |  | anc_allele | STRING | The reported ancestral allele if there is one.
 |  | rms_bq | FLOAT | The RMS base quality at this position.
 |  | cigar | STRING | CIGAR string describing how to align an alternate allele to the reference allele.
 |  | depth | INTEGER | The number of aligned sequence reads that led to this variant call
 |  | strand_bias | FLOAT | Strand bias at the variant position
 |  | rms_map_qual | FLOAT | RMS mapping quality, a measure of variance of quality scores
 |  | in_hom_run | INTEGER | Homopolymer runs for the variant allele
 |  | num_mapq_zero | INTEGER | Total counts of reads with mapping quality equal to zero
 |  | num_alleles | INTEGER | Total number of alleles in called genotypes
 |  | [NAME] | FLOAT | Fraction of reads with spanning deletions
 |  | haplotype_score | FLOAT | Consistency of the site with two segregating haplotypes
 |  | qual_depth | FLOAT | Variant confidence or quality by depth
 |  | allele_count | INTEGER | Allele counts in genotypes
 |  | allele_bal | FLOAT | Allele balance for hets
 |  | is_somatic | BOOL | Whether the variant is somatically acquired.
Population Frequency information |  | in_dbsnp | BOOL | Is this variant found in dbSnp (build 135)?
 |  |  |  | 0 : Absence of the variant in dbsnp
 |  |  |  | 1 : Presence of the variant in dbsnp
 |  | rs_ids | STRING | A comma-separated list of rs ids for variants present in dbsnp
 |  | in_hm2 | BOOL | Whether the variant was part of HapMap2.
 |  | in_hm3 | BOOL | Whether the variant was part of HapMap3.
 |  | in_esp | BOOL | Presence/absence of the variant in the ESP project data
 |  | [NAME] | BOOL | Presence/absence of the variant in the 1000 genome project data
 |  | aaf_esp_ea | FLOAT | Minor [NAME] of the variant for European Americans in the ESP project
 |  | aaf_esp_aa | FLOAT | Minor [NAME] of the variant for African Americans in the ESP project
 |  | aaf_esp_all | FLOAT | Minor [NAME] of the variant w.r.t both groups in the ESP project
 |  | aaf_1kg_amr | FLOAT | [NAME] of the variant for samples in AMR based on AC/AN (1000g project)
 |  | aaf_1kg_asn | FLOAT | Allele frequency of the variant for samples in ASN based on AC/AN (1000g project)
 |  | aaf_1kg_afr | FLOAT | Allele frequency of the variant for samples in AFR based on AC/AN (1000g project)
 |  | aaf_1kg_eur | FLOAT | [NAME] of the variant for samples in EUR based on AC/AN (1000g project)
 |  | aaf_1kg_all | FLOAT | Global allele frequency (based on AC/AN) (1000g project)
Disease Phenotype Information |  | [NAME] | BOOL | 0 : Absence of the variant in OMIM database
 |  |  |  | 1 : Presence of the variant in OMIM database
 |  | clinvar_sig | STRING | The clinical significance scores for each
 |  |  |  | of the variant according to ClinVar:
 |  |  |  | unknown, untested, non-pathogenic
 |  |  |  | probable-non-pathogenic, probable-pathogenic
 |  |  |  | pathogenic, drug-response, histocompatibility
 |  |  |  | other
 |  | clinvar_disease_name | STRING | The name of the disease to which the variant is relevant
 |  | clinvar_dbsource | STRING | Variant Clinical Channel IDs
 |  | clinvar_dbsource_id | STRING | The record id in the above database
 |  | clinvar_origin | STRING | The type of variant.
 |  |  |  | Any of:
 |  |  |  | unknown, germline, somatic,
 |  |  |  | inherited, paternal, maternal,
 |  |  |  | de-novo, biparental, uniparental,
 |  |  |  | not-tested, tested-inconclusive,
 |  |  |  | other
 |  | clinvar_dsdb | STRING | Variant disease database name
 |  | clinvar_dsdbid | STRING | Variant disease database ID
 |  | clinvar_disease_acc | STRING | Variant Accession and Versions
 |  | clinvar_in_locus_spec_db | BOOL | Submitted from a locus-specific database?
 |  | clinvar_on_diag_assay | BOOL | Variation is interrogated in a clinical diagnostic assay?
Genome Annotations |  | exome_chip | BOOL | Whether an SNP is on the Illumina HumanExome Chip
 |  | cyto_band | STRING | Chromosomal cytobands that a variant overlaps
 |  | rmsk | STRING | A comma-separated list of RepeatMasker annotations that the variant overlaps.
 |  |  |  | Each hit is of the form: name_class_family
 |  | in_cpg_island | BOOL | Does the variant overlap a CpG island?.
 |  |  |  | Based on UCSC: Regulation > CpG Islands > cpgIslandExt
 |  | in_segdup | BOOL | Does the variant overlap a segmental duplication?.
 |  |  |  | Based on UCSC: Variation&Repeats > Segmental Dups > genomicSuperDups track
 |  | is_conserved | BOOL | Does the variant overlap a conserved region?
 |  |  |  | Based on the 29-way mammalian conservation study
 |  | gerp_bp_scpre | FLOAT | GERP conservation score.
 |  |  |  | Only populated if the --load-gerp-bp option is used when loading.
 |  |  |  | Higher scores reflect greater conservation. At base-pair resolution.
 |  |  |  | Details: http://mendel.stanford.edu/SidowLab/downloads/gerp/
 |  | gerp_element_pval | FLOAT | GERP elements P-val
 |  |  |  | Lower P-values scores reflect greater conservation. Not at base-pair resolution.
 |  |  |  | Details: http://mendel.stanford.edu/SidowLab/downloads/gerp/
 |  | recomb_rate | FLOAT | Returns the mean recombination rate at the variant site
 |  |  |  | Based on HapMapII_GRCh37 genetic map
Functional annotations from ENCODE |  | grc | STRING | Association with patch and fix regions from the Genome Reference Consortium:
 |  |  |  | http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
 |  |  |  | Identifies potential problem regions associated with variant calls.
 |  |  |  | Built with annotation_provenance/make-ncbi-grc-patches.py
 |  | gms_illumina | FLOAT | Genome Mappability Scores (GMS) for Illumina error models
 |  |  |  | Provides low GMS scores (< 25.0 in any technology) from:
 |  |  |  | http://sourceforge.net/apps/mediawiki/gma-bio/index.php?title=Download_GMS
 |  |  |  | #Download_GMS_by_Chromosome_and_Sequencing_Technology
 |  |  |  | Input VCF for annotations prepared with:
 |  |  |  | https://github.com/chapmanb/bcbio.variation/blob/master/src/bcbio/variation/utils/gms.clj
 |  | gms_solid | FLOAT | Genome Mappability Scores with SOLiD error models
 |  | gms_iontorrent | FLOAT | Genome Mappability Scores with IonTorrent error models
 |  | encode_tfbs | STRING | Comma-separated list of transcription factors that were
 |  |  |  | observed by ENCODE to bind DNA in this region. Each hit in the list is constructed
 |  |  |  | as TF_CELLCOUNT, where:
 |  |  |  | TF is the transcription factor name
 |  |  |  | CELLCOUNT is the number of cells tested that had nonzero signals.
 |  |  |  | Provenance: wgEncodeRegTfbsClusteredV2 UCSC table
 |  | encode_dnaseI_cell_count | INTEGER | Count of cell types that were observed to have DnaseI hypersensitivity.
 |  | encode_dnaseI_cell_list | STRING | Comma separated list of cell types that were observed to have DnaseI hypersensitivity.
 |  |  |  | Provenance: [NAME], et [NAME], Nature, 489, pp. 75-82, 5 Sep. 2012
 |  | encode_consensus_gm12878 | STRING | ENCODE consensus segmentation prediction for GM12878.
 |  |  |  | CTCF: CTCF-enriched element
 |  |  |  | E: Predicted enhancer
 |  |  |  | PF: Predicted promoter flanking region
 |  |  |  | R: Predicted repressed or low-activity region
 |  |  |  | TSS: Predicted promoter region including TSS
 |  |  |  | T: Predicted transcribed region
 |  |  |  | WE: Predicted weak enhancer or open chromatin cis-regulatory element | unknown: This region of the genome had no functional prediction.
 |  | encode_consensus_h1hesc | STRING | ENCODE consensus segmentation prediction for h1HESC. See encode_consseg_gm12878 for details.
 |  | encode_consensus_helas3 | STRING | ENCODE consensus segmentation prediction for Helas3. See encode_consseg_gm12878 for details.
 |  | encode_consensus_hepg2 | STRING | ENCODE consensus segmentation prediction for HEPG2. See encode_consseg_gm12878 for details.
 |  | encode_consensus_huvec | STRING | ENCODE consensus segmentation prediction for HuVEC. See encode_consseg_gm12878 for details.
 |  | encode_consensus_k562 | STRING | ENCODE consensus segmentation prediction for k562. See encode_consseg_gm12878 for details.