The GEMINI database schema

The variants table

Core VCF fields

column_name type notes
chrom STRING The chromosome on which the variant resides (from VCF CHROM field).
start INTEGER The 0-based start position. (from VCF POS field, but converted to 0-based coordinates)
end INTEGER The 1-based end position. (from VCF POS field, yet inferred based on the size of the variant)
vcf_id STRING The VCF ID field.
variant_id INTEGER PRIMARY_KEY
anno_id INTEGER Variant transcript number for the most severely affected transcript
ref STRING Reference allele (from VCF REF field)
alt STRING Alternate allele for the variant (from VCF ALT field)
qual INTEGER Quality score for the assertion made in ALT (from VCF QUAL field)
filter STRING A string of filters passed/failed in variant calling (from VCF FILTER field)

Variant and PopGen 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
hwe FLOAT The Chi-square 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

Genotype information

     
gts BLOB
A compressed binary vector of sample genotypes (e.g., “A/A”, “A|G”, “G/G”)
- Extracted from the VCF GT genotype tag.
gt_types BLOB
A compressed binary vector of numeric genotype “types” (e.g., 0, 1, 2)
- Inferred from the VCF GT genotype tag.
gt_phases BLOB
A compressed binary vector of sample genotype phases (e.g., False, True, False)
- Extracted 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 BLOB
A compressed binary vector of the depth of aligned sequence observed for each sample
- Extracted from the VCF DP genotype tag.
gt_ref_depths BLOB
A compressed binary vector of the depth of reference alleles observed for each sample
- Extracted from the VCF AD genotype tag.
gt_alt_depths BLOB
A compressed binary vector of the depth of alternate alleles observed for each sample
- Extracted from the VCF AD genotype tag.
gt_quals BLOB
A compressed binary vector of the genotype quality (PHRED scale) estimates for each sample
- Extracted from the VCF GQ genotype tag.
gt_phred_ll_homref BLOB
A compressed binary vector of the phred-scaled genotype likelihood of the 0/0 genotype estimates for each sample
- Extracted from the VCF GL or PL tag.
- New in version 0.13.0
gt_phred_ll_het BLOB
A compressed binary vector of the phred-scaled genotype likelihood of the 0/1 genotype estimates for each sample
- Extracted from the VCF GL or PL tag.
- New in version 0.13.0
gt_phred_ll_homalt BLOB
A compressed binary vector of the phred-scaled genotype likelihood of the 1/1 genotype estimates for each sample
- Extracted from the VCF GL or PL tag.
- New in version 0.13.0

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, the protein_coding biotype is prioritized (SnpEff/VEP)
is_exonic BOOL Does the variant affect an exon for >= 1 transcript?
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 LOF for >= transcript?
is_splicing BOOL Does the variant affect a canonical or possible splice site? That is, set to TRUE if the SO term is any of splice_acceptor_variant, splice_donor_variant, or splice_region_variant.
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 a 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_so STRING The Sequence ontology term for the most severe consequence
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 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. From the “SB” tag.
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
num_reads_w_dels 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
info BLOB Stores the INFO field of the VCF

Population information

     
in_dbsnp BOOL
Is this variant found in dbSNP?
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
in_1kg BOOL Presence/absence of the variant in the 1000 genome project data (phase 3)
aaf_esp_ea FLOAT Minor Allele Frequency of the variant for European Americans in the ESP project
aaf_esp_aa FLOAT Minor Allele Frequency of the variant for African Americans in the ESP project
aaf_esp_all FLOAT Minor Allele Frequency of the variant w.r.t both groups in the ESP project
aaf_1kg_amr FLOAT Allele frequency of the variant in AMR population based on AC/AN (1000g project, phase 3)
aaf_1kg_eas FLOAT Allele frequency of the variant in EAS population based on AC/AN (1000g project, phase 3)
aaf_1kg_sas FLOAT Allele frequency of the variant in SAS population based on AC/AN (1000g project, phase 3)
aaf_1kg_afr FLOAT Allele frequency of the variant in AFR population based on AC/AN (1000g project, phase 3)
aaf_1kg_eur FLOAT Allele frequency of the variant in EUR population based on AC/AN (1000g project, phase 3)
aaf_1kg_all FLOAT Global allele frequency (based on AC/AN) (1000g project - phase 3)
in_exac BOOL Presence/absence of the variant in ExAC (Exome Aggregation Consortium) data (Broad)
aaf_exac_all FLOAT Raw allele frequency (population independent) of the variant based on ExAC exomes (AF)
aaf_adj_exac_all FLOAT Adjusted allele frequency (population independent) of the variant based on ExAC (Adj_AC/Adj_AN)
aaf_adj_exac_afr FLOAT Adjusted allele frequency of the variant for AFR population in ExAC (AC_AFR/AN_AFR)
aaf_adj_exac_amr FLOAT Adjusted allele frequency of the variant for AMR population in ExAC (AC_AMR/AN_AMR)
aaf_adj_exac_eas FLOAT Adjusted allele frequency of the variant for EAS population in ExAC (AC_EAS/AN_EAS)
aaf_adj_exac_fin FLOAT Adjusted allele frequency of the variant for FIN population in ExAC (AC_FIN/AN_FIN)
aaf_adj_exac_nfe FLOAT Adjusted allele frequency of the variant for NFE population in ExAC (AC_NFE/AN_NFE)
aaf_adj_exac_oth FLOAT Adjusted allele frequency of the variant for OTH population in ExAC (AC_OTH/AN_OTH)
aaf_adj_exac_sas FLOAT Adjusted allele frequency of the variant for SAS population in ExAC (AC_SAS/AN_SAS)
max_aaf_all FLOAT the maximum of aaf_esp_ea, aaf_esp_aa, aaf_1kg_amr, aaf_1kg_eas,aaf_1kg_sas,aaf_1kg_afr,aaf_1kg_eur,aaf_adj_exac_afr,aaf_adj_exac_amr,aaf_adj_exac_eas,aaf_adj_exac_nfe,aaf_adj_exac_sas. and -1 if none of those databases/populations contain the variant.
exac_num_het INTEGER The number of heterozygote genotypes observed in ExAC. Pulled from the ExAC AC_Het INFO field.
exac_num_hom_alt INTEGER The number of homozygous alt. genotypes observed in ExAC. Pulled from the ExAC AC_Het INFO field.
exac_num_chroms INTEGER The number of chromosomes underlying the ExAC variant call. Pulled from the ExAC AN_Adj INFO field.

Disease phenotype info (from ClinVar).

     
in_omim BOOL
0 : Absence of the variant in OMIM database
1 : Presence of the variant in OMIM database
clinvar_causal_allele STRING The allele(s) that are associated or causal for the disease.
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?
clinvar_gene_phenotype STRING ‘|’ delimited list of phenotypes associated with this gene (includes any variant in the same gene in clinvar not just the current variant).
geno2mp_hpo_ct INTEGER Value from geno2mp indicating count of HPO profiles. Set to -1 if missing

Structural variation columns

     
sv_cipos_start_left INTEGER The leftmost position of the leftmost SV breakpoint confidence interval.
sv_cipos_end_left INTEGER The rightmost position of the leftmost SV breakpoint confidence interval.
sv_cipos_start_right INTEGER The leftmost position of the rightmost SV breakpoint confidence interval.
sv_cipos_end_right INTEGER The rightmost position of the rightmost SV breakpoint confidence interval.
sv_length INTEGER The length of the structural variant in base pairs.
sv_is_precise BOOL Is the structural variant precise (i.e., to 1-bp resolution)?
sv_tool STRING The name of the SV discovery tool used to find the SV.
sv_evidence_type STRING What type of alignment evidence supports the SV?
sv_event_id STRING A unique identifier for the SV.
sv_mate_id STRING The ID for the “other end” of the SV.
sv_strand STRING The orientations of the SV breakpoint(s).

Genome annotations

     
exome_chip BOOL Whether a 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_score 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.
gerp_element_pval FLOAT
GERP elements P-val
Lower P-values scores reflect greater conservation. Not at base-pair resolution.
recomb_rate FLOAT
Returns the mean recombination rate at the variant site
Based on HapMapII_GRCh37 genetic map
cadd_raw FLOAT
Raw CADD scores for scoring deleteriousness of SNV’s in the human genome
cadd_scaled FLOAT
Scaled CADD scores (Phred like) for scoring deleteriousness of SNV’s
fitcons FLOAT
fitCons scores estimating the probability that a point mutation
at each position in a genome will influence fitness.
Higher scores have more potential for interesting genomic function.
Common ranges: 0.05-0.35 for non-coding and 0.4-0.8 for coding
Provides integerated highly significant scores (i6-0).

Note: CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (mccullaj@uw.edu).

Variant error assessment

     
grc STRING
Association with patch and fix regions from the Genome Reference Consortium:
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:
#Download_GMS_by_Chromosome_and_Sequencing_Technology
Input VCF for annotations prepared with:
gms_solid FLOAT Genome Mappability Scores with SOLiD error models
gms_iontorrent FLOAT Genome Mappability Scores with IonTorrent error models
in_cse BOOL
Is a variant in an error prone genomic position,
using CSE: Context-Specific Sequencing Errors

ENCODE information

     
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: Thurman, et al, 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.
vista_enhancers STRING Experimentally validated human enhancers from VISTA (http://enhancer.lbl.gov/frnt_page_n.shtml)

The variant_impacts table

column_name type notes
variant_id INTEGER PRIMARY_KEY (Foreign key to variants table)
anno_id INTEGER PRIMARY_KEY (Based on variant transcripts)
gene STRING The gene affected by the variant.
transcript STRING The transcript affected by the variant.
is_exonic BOOL Does the variant affect an exon for this transcript?
is_coding BOOL Does the variant fall in a coding region (excludes 3’ & 5’ UTR’s of exons)?
is_lof BOOL Based on the value of the impact col, is the variant LOF?
exon STRING Exon information for the variants that are exonic
codon_change STRING What is the codon change?
aa_change STRING What is the amino acid change?
aa_length STRING The length of CDS in terms of number of amino acids (SnpEff only)
biotype STRING The type of transcript (e.g., protein-coding, pseudogene, rRNA etc.) (SnpEff only)
impact STRING Impacts due to variation (ref.impact category)
impact_so STRING The sequence ontology term for the impact
impact_severity STRING Severity of the impact based on the impact column value (ref.impact category)
polyphen_pred STRING
Impact of the SNP as given by PolyPhen (VEP only)
benign, possibly_damaging, probably_damaging, unknown
polyphen_scores FLOAT Polyphen score reflecting severity (higher the impact, higher the score) (VEP only)
sift_pred STRING
Impact of the SNP as given by SIFT (VEP only)
neutral, deleterious
sift_scores FLOAT SIFT prob. scores reflecting severity (Higher the impact, lower the score) (VEP only)

Details of the impact and impact_severity columns

impact severity impacts SO_impacts
HIGH
  • exon_deleted
  • frame_shift
  • splice_acceptor
  • splice_donor
  • start_loss
  • stop_gain
  • stop_loss
  • non_synonymous_start
  • transcript_codon_change
  • rare_amino_acid
  • chrom_large_del
MED
  • non_syn_coding
  • inframe_codon_gain
  • inframe_codon_loss
  • inframe_codon_change
  • codon_change_del
  • codon_change_ins
  • UTR_5_del
  • UTR_3_del
  • splice_region
  • mature_miRNA
  • regulatory_region
  • TF_binding_site
  • regulatory_region_ablation
  • regulatory_region_amplification
  • TFBS_ablation
  • TFBS_amplification
LOW
  • synonymous_stop
  • synonymous_coding
  • UTR_5_prime
  • UTR_3_prime
  • intron
  • CDS
  • upstream
  • downstream
  • intergenic
  • intragenic
  • gene
  • transcript
  • exon
  • start_gain
  • synonymous_start
  • intron_conserved
  • nc_transcript
  • NMD_transcript
  • incomplete_terminal_codon
  • nc_exon
  • transcript_ablation
  • transcript_amplification
  • feature elongation
  • feature truncation

The samples table

column name type notes
sample_id INTEGER PRIMARY_KEY
name STRING Sample names
family_id INTEGER Family ids for the samples [User defined, default: NULL]
paternal_id INTEGER Paternal id for the samples [User defined, default: NULL]
maternal_id INTEGER Maternal id for the samples [User defined, default: NULL]
sex STRING Sex of the sample [User defined, default: NULL]
phenotype STRING The associated sample phenotype [User defined, default: NULL]
ethnicity STRING The ethnic group to which the sample belongs [User defined, default: NULL]

The resources table

Establishes provenance of annotation resources used to create a GEMINI database.

column name type notes
name STRING Name of the annotation type
resource STRING Filename of the resource, with version information

The version table

Establishes which version of gemini was used to create a database.

column name type notes
version STRING What version of gemini was used to create the DB.

The gene_detailed table

Built on version 75 of Ensembl genes

column_name type notes
uid INTEGER PRIMARY_KEY (unique identifier for each entry in the table)
chrom STRING The chromosome on which the gene resides
gene STRING The gene name
is_hgnc BOOL Flag for gene column: 0 for non HGNC symbol and 1 for HGNC symbol = TRUE
ensembl_gene_id STRING The ensembl gene id for the gene
transcript STRING The ensembl transcript id for the gene
biotype STRING The biotype (e.g., protein coding) of the transcript
transcript_status STRING The status of the transcript (e.g. KNOWN, PUTATIVE etc.)
ccds_id STRING The consensus coding sequence transcript identifier
hgnc_id STRING The HGNC identifier for the gene if HGNC symbol is TRUE
entrez_id STRING The entrez gene identifier for the gene
cds_length STRING The length of CDS in bases
protein_length STRING The length of the transcript as the number of amino acids
transcript_start STRING The start position of the transcript in bases
transcript_end STRING The end position of the transcript in bases
strand STRING The strand of DNA where the gene resides
synonym STRING Other gene names (previous or synonyms) for the gene
rvis_pct FLOAT The RVIS percentile values for the gene
mam_phenotype_id STRING
High level mammalian phenotype ID applied to mouse phenotype descriptions

The gene_summary table

Built on version 75 of Ensembl genes

column_name type notes
uid INTEGER PRIMARY_KEY (unique identifier for each entry in the table)
chrom STRING The chromosome on which the gene resides
gene STRING The gene name
is_hgnc BOOL Flag for gene column: 0 for non HGNC symbol and 1 for HGNC symbol = TRUE
ensembl_gene_id STRING The ensembl gene id for the gene
hgnc_id STRING The HGNC identifier for the gene if HGNC symbol is TRUE
transcript_min_start STRING The minimum start position of all transcripts for the gene
transcript_max_end STRING The maximum end position of all transcripts for the gene
strand STRING The strand of DNA where the gene resides
synonym STRING Other gene names (previous or synonyms) for the gene
rvis_pct FLOAT The RVIS percentile values for the gene
mam_phenotype_id STRING
High level mammalian phenotype ID applied to mouse phenotype descriptions
in_cosmic_census BOOL Are mutations in the gene implicated in cancer by the cancer gene census?
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