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

BMC Medical Genomics

Table 2 Summary of NA12878 individual analysis

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

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.

ISSN: 1755-8794