Table 4.
Variants count with functional annotation of noncoding variants.
| Variants filtering | Variant count | |
|---|---|---|
| FilterMutectCalls | Total: 1,583,400 (SNPs: 1,282,284; MNPs: 47,693; Indels: 253,423) | |
| < .01 AF 1000G ALL and non-TCGA ExAC ALL | 1,467,158 (SNPs: 1,215,768; MNPs: 47,693; Indels: 203,697) | |
| CADD (SNPs) or CADD Indel (indels) Scaled Phred Score > 10 | 143,719 (SNPs: 134,929; MNPs: 2386; Indels: 6404) | |
| Variant stratification | Coding Variants | Non-Coding Variants |
| Total count | 9494 | 134,225 |
| Predicted deleterious by at least 3 of MutationTaster, PolyPhen V2, Provean and SIFT | 3196 | NA |
| Exclusive to a particular group | Total: (G1: 2139; G2: 1048) | Total: (G1: 78,704; G2: 38,845) |
| Shared by at least 2 subjects in same group | Total: (G1: 6; G2: 4) | Total: (G1: 3992; G2: 1144) |
| FunSeq2 Score > = 1.5 | NA | Total: (G1: 12; G2: 3) |
| Functional annotation of noncoding variants (FunSeq2 Score > = 1.5) according to ANNOVAR | ||
| Variants annotation according to region hit from RefSeq | G1 | G2 |
| Intergenic | 2 | 0 |
| Intronic | 5 | 2 |
| ncRNA_intronic | 1 | 0 |
| 3’UTR | 0 | 0 |
| Upstream and Downstream | 2 | 1 |
| 5’UTR5 | 2 | 0 |
| ncRNA_exonic | 0 | 0 |
Bold indicates final variant count after filtering.
RefSeq Reference sequence database, ncRNA non-coding transcript variant, NA Not Applicable, ExAC Exome aggregation consortium, AF Allele Frequency, 1000G 1000 Genomes project for all individuals in this release, CADD Combined Annotation Dependent Depletion, SNPs Single Nucleotide Polymorphisms, Indels insertions/deletions, MNPS Multi-nucleotide Polymorphisms, PolyPhen V2 PolyPhen Version 2, G1 positive-positive subjects, G2 positive–negative subjects, SIFT Sorting Intolerant From Tolerant, PROVEAN Protein Variation Effect Analyzer.