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Table 1 Summary of 1,000 Genomes Project dataset analysis

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

Individual ID DNA mean coverage RNA mean coverage Het SNPs Available genes ASE genes Imprinted available genes Imprinted ASE genes Fisher p-value
NA06994 98 46 7397 1896 94 (5%) 7 2 (28%) 0.04
NA07357 71 139 7904 1889 71 (3.8%) 9 2 (22%) 0.04
NA10847 105 104 7490 1877 101 (5.4%) 5 1 (20%) 0.2
NA11831 74 126 7604 2002 101 (5%) 3 0 -
NA11843 55 136 7361 1694 77 (4.5%) 4 1 (25%) 0.2
NA11894 148 107 6385 1683 91 (5.4%) 2 2 (100%) 0.003
NA11930 58 149 7320 1662 47 (2.8%) 7 3 (30%) 0.0008
NA11992 84 90 7724 1744 58 (3.3%) 6 0 -
NA12004 59 94 7562 1544 48 (3.1%) 3 1 (33%) 0.09
NA12043 108 77 7759 1838 91 (5%) 5 1 (20%) 0.2
NA12045 81 122 7419 1841 58 (3.2%) 3 0 -
NA12144 87 81 7844 2020 92 (4.6%) 7 2 (28%) 0.04
NA12155 83 113 7940 1802 87 (4.8%) 4 2 (50%) 0.01
NA12286 107 100 7572 1767 86 (4.9%) 8 2 (25%) 0.06
NA12348 134 124 6408 1400 50 (3.6%) 4 2 (50%) 0.008
NA12717 101 77 7467 1857 93 (5%) 4 1 (25%) 0.2
NA12750 118 89 8623 1972 108 (5.5%) 4 1 (25%) 0.2
NA12751 99 111 7396 2115 97 (4.6%) 5 3 (60%) 0.001
NA12842 182 141 7728 2074 163 (7.9%) 7 2 (28%) 0.1
NA12874 69 129 7297 1738 85 (4.9%) 4 1 (25%) 0.2
Average 96.05 107.75 7510 1820.75 84.9 (4.6%) 5.05 1.45 (29%) -
  1. For each individual 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. Finally, we report the number of imprinted genes we found available for ASE calculation, the number of these that are identified as ASE genes and the p-values obtained by testing the significance of proportion of imprinted ASE genes with respect to the overall ASE genes proportion (no test is performed when 0 imprinted ASE genes are detected).