| VariantID |
Variant identifier [#chr]_[genomicposition]_[RefBase]_[VarBase] |
| Gene |
Gene symbol |
| omimId |
OMIM® id |
| TranscriptID |
RefSeq transcript id |
| TranscriptLength |
Length of transcript (full cDNA length) |
| Chr |
Chromosome of variant |
| Start |
Start position of variant |
| End |
End position of variant |
| Ref |
Nucleotide sequence in the reference genome (restricted to 50bp) |
| Mut |
Alternate nucleotide sequence (restricted to 50bp) |
| Uniprot |
Uniprot |
| protein |
Protein id (NCBI) |
| posAA |
Amino acid position |
| wtAA_1 |
Reference codon |
| varAA_1 |
Alternate codon |
| Phred_QUAL |
QUAL: The Phred scaled probability that a REF/ALT polymorphism exists at this site given sequencing data. Because the Phred scale is −10 * log(1 − p), a value of 10 indicates a 1 in 10 chance of error, while a 100 indicates a 1 in chance. These values can grow very large when a large amount of NGS data is used for variant calling. |
| HomHet |
Homozygote or heterozygote status |
| TotalReadDepth |
Total number of reads covering the position |
| VarReadDepth |
Number of reads supporting the variant |
| %Reads_variation |
Percent of reads supporting variant over those supporting reference sequence/base |
| VarType |
Variant Type (substitution, deletion, insertion, duplication, delins) |
| CodingEffect |
Variant Coding effect (synonymous, missense, nonsense, in-frame, frameshift, start loss, stop loss) |
| VarLocation |
Variant location (upstream, 5’UTR, exon, intron, 3’UTR, downstream) |
| Exon |
Exon (nearest exon if intronic variant) |
| Intron |
Intron |
| gNomen |
Genomic-level nomenclature |
| cNomen |
cDNA-level nomenclature |
| pNomen |
Protein-level nomenclature |
| rsID |
dbSNP variation |
| rsValidation |
dbSNP validated status |
| rsClinicalSignificance |
dbSNP variation clinical significance |
| rsAncestralAllele |
dbSNP ancestral allele |
| rsHeterozygosity |
dbSNP variation average heterozygosity |
| rsMAF |
dbSNP variation global Minor Allele |
| rsMAFAllele |
dbSNP variation global minor allele |
| rsMAFCount |
dbSNP variation sample size |
| 1000g_AF |
1,000 genomes global allele frequency |
| 1000g_AFR_AF |
1,000 genomes allele frequency in African population |
| 1000g_SAS_AF |
1,000 genomes allele frequency in South Asian population |
| 1000g_EAS_AF |
1,000 genomes allele frequency in East Asian population |
| 1000g_EUR_AF |
1,000 genomes allele frequency in European population |
| espRefEACount |
ESP reference allele count in European American population |
| espRefAACount |
ESP reference allele count in African American population |
| espRefAllCount |
ESP reference allele count in all population |
| espAltEACount |
ESP alternate allele count in European American population |
| espAltAACount |
ESP alternate allele count in African American population |
| espAltAllCount |
ESP alternate allele count in all population |
| espEAMAF |
Minor allele frequency in European American population |
| espAAMAF |
Minor allele frequency in African American population |
| espAllMAF |
Minor allele frequency in all population |
| espAvgReadDepth |
Average sample read Depth |
| delta MESscore (%) |
% difference between the splice score of variant with the score of the reference base |
| wtMEScore |
WT seq. MaxEntScan score |
| varMEScore |
Variant seq. MaxEntScan score |
| delta SSFscore (%) |
% difference between the splice score of variant with the score of the reference base |
| wtSSFScore |
WT seq. SpliceSiteFinder score |
| varSSFScore |
Variant seq. SpliceSiteFinder score |
| delta NNSscore (%) |
% difference between the splice score of variant with the score of the reference base |
| wtNNSScore |
WT seq. NNSPLICE score |
| varNNSScore |
Variant seq. NNSPLICE score |
| DistNearestSS |
Distance to Nearest splice site |
| NearestSS |
Nearest splice site |
| localSpliceEffect |
Splicing effect in variation vicinity (New donor Site, New Acceptor Site, Cryptic Donor Strongly Activated, Cryptic Donor Weakly Activated, Cryptic Acceptor Strongly Activated, Cryptic Acceptor Weakly Activated) |
| SiftPred |
SIFT prediction |
| SiftWeight |
SIFT score ranges from 0 to 1. The amino acid substitution is predicted damaging is the score is <=0.05, and tolerated if the score is >0.05. |
| SiftMedian |
SIFT median ranges from 0 to 4.32. This is used to measure the diversity of the sequences used for prediction. A warning will occur if this is greater than 3.25 because this indicates that the prediction was based on closely related sequences. The number should be between 2.75 and 3.5 |
| PPH2pred |
PolyPhen-2 prediction using HumVar model are either “neutral, possibly damaging, probably damaging” or “neutral, deleterious” depending on the annotation engine. |
| phyloP |
phyloP |
| PhastCons |
PhastCons score |
| GranthamDist |
Grantham distance |
| VaRank_VarScore |
Prioritization score according to VaRank |
| AnnotationAnalysis |
Yes or No indicates if the variation could annotated by any annotation engine |
| Avg_TotalDepth |
Total read depth average at the variant position for all samples analyzed that have the variation |
| SD_TotalDepth |
Standard deviation associated with Avg_TotalDepth |
| Count_TotalDepth |
Number of samples considered for the average total read depth |
| Avg_SNVDepth |
Variation read depth average at the variant position for all samples analyzed that have the variation |
| SD_SNVDepth |
Standard deviation associated with Avg_SNVDepth |
| Count_SNVDepth |
Number of samples considered for the average SNV read depth |
| familyBarcode |
Homozygote or heterozygote status for the sample of interest and its associated samples |
| Barcode |
Homozygote or heterozygote status for all sample analyzed together (Hom: 2; Het: 1; Sample name is given at the first line of the file: ## Barcode) |
| Hom_Count |
Number of homozygote over all samples analyzed together |
| Het_Count |
Number of heterozygote over all samples analyzed together |
| Allele_Count |
Number of alleles supporting the variant |
| Sample_Count |
Total number of samples |
