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Table 2 Summary of NA12878 individual analysis

From: ASEQ: fast allele-specific studies from next-generation sequencing data

Input SNP list DNA mean coverage RNA mean coverage Het SNPs Available genes ASE genes Available imprinted genes Imprinted ASE genes
1,000 Genomes Project 88 39 16016 3071 184 (6%) 10 1
Coding dbsnp 138 100 41 7465 2403 169 (7%) 9 2
Exon dbsnp138 90 40 9372 2840 203 (7.1%) 13 4
  1. We report ASE analysis results on NA12878 individual for all combinations of input SNP list considered. For each combination we report the mean coverage in WES and RNA-seq data computed at SNP positions and the number of heterozygous SNPs identified from WES. Then we report the number of genes found available for ASE calculation along with the number of genes identified as ASE genes with corresponding percentages. We also report the number of imprinted genes we found available for ASE calculation and the number of these that are identified as ASE genes.