Columns

Preview columns

Column	Field	Description
family	familyId	Family ID
	study	Study name
variant	location	The position of the variant in a 1-­‐based coordinate system of hg19 reference assembly.
	variant	Description of the variant: sub(R-­‐>A) stands for substitution of the reference allele R to an alternative allele A; ins(seq) stands for insertion of the provided sequence (“seq”), and del(N) stands for deletions of N nucleotides

Download columns

Field	Description
familyId	Family ID
study	Study name
phenotype	Study phenotype
location	The position of the variant in a 1-­‐based coordinate system of hg19 reference assembly.
variant	Description of the variant: sub(R-­‐>A) stands for substitution of the reference allele R to an alternative allele A; ins(seq) stands for insertion of the provided sequence (“seq”), and del(N) stands for deletions of N nucleotides
family genotype	The best state according to the Multinomial Model (Experimental Procedures). The format of the column is “momR dadR autR sibR/momA dadA autA sibA” where (for example) momR stands for the number of copies of the reference allele in the mother’s genotype and autA stands for the number of copies of the alternative allele in the genotype of the affected child.
family structure
from parent	Shows the parental haplotypes giving rise to de novo variants when they could be identified.
in child	Shows the affected status and gender of the child in which the de novo variant was observed. The two children are listed when the de novo variant is shared by both.
count	The observed number of reads supporting the different alleles at a given location. The format is <reference allele counts>/<alternative allele counts>/<other allele counts> and the order of individuals is <mom> <dad> <proband> and <sibling>. For example, “10 12 5 20/1 0 8 0/0 0 0 1” indicates that there were 10 reads supporting the reference allele in the mother, there were 8 reads supporting the alternative in the proband, and there was 1 read with a non-­‐reference allele in the unaffected sibling.
alt alleles
parents called	Count of independent parents tested for this variant
worst effect type	The most severe effect the variant has on genes.
genes	The list of gene affected by the variant and the most severe effect for every gene. The format is <gene 1>:<effect on gene 1>|<gene 2>:<effect on gene 2>|.
all effects
effect details	Details of variant effects on each affected isoform. The format is: <isoform 1 of gene 1>; <isoform 2 or gene 1>|<isoform 1 of gene 2>; <isoform 2 of gene 2>|… The amino acid change and the position of the amino acid within the protein are shown.