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Table 2 Statistical attributes of whole gene GenePy scores computed for sixteen deleteriousness metrics. Number of genes for which GenePy scores were calculated, median number of non-variant genes (GenePy = 0), mean GenePy scores, mean and standard deviation across our cohort (n = 508), coefficient of variation (CV, defined as σ/μ) and the median number of genes with a GenePy score < 0,01 as percentage of the total number of genes. The same information is reported for GenePycgl

From: GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data

Metric Gene scores calculated aMedian no. of genes with GenePy = 0 within individuals (%) Max GenePy MeanGenePy CV uncorrected Median no. of genes with GenePy < 0.01 within individuals (%) Max GenePycgl Mean GenePycgl CVcgl corrected Median no. of genes with Genepycgl < 0.01(%)
CADD 14,184 9917 (69.92%) 32.15 0.10 3.81 10,231 (72.13%) 74.19 0.08 8.09 10,304 (72.64%)
DANN 14,184 9917 (69.92%) 110.48 0.33 3.37 10,153 (71.58%) 304.15 0.25 6.96 10,196 (71.88%)
FATHMM 13,143 9981 (75.94%) 72.73 0.16 4.15 10,923 (83.11%) 269.62 0.11 6.42 11,092 (84.40%)
fathmm-MKL 14,178 9039 (63.75%) 50.10 0.16 3.29 9282 (65.48%) 131.34 0.12 7.55 9332 (65.84%)
GERP++_RS 14,197 9910 (69.80%) 100.44 0.32 3.35 10,116 (71.25%) 283.69 0.24 6.47 10,143 (71.44%)
M-CAP 12,921 12,577 (97.34%) 24.52 0.02 12.65 12,596 (97.48%) 59.88 0.02 19.05 12,630 (97.74%)
MetaLR 14,063 12,752 (90.68%) 38.14 0.04 8.77 13,146 (93.48%) 87.80 0.04 16.14 13,253 (94.24%)
MetaSVM 14,076 9845 (69.94%) 36.76 0.10 3.95 10,141 (72.04%) 99.44 0.08 8.94 10,207 (72.51%)
MutationTaster 14,039 12,161 (86.62%) 90.86 0.13 5.24 12,521 (89.19%) 332.05 0.09 9.02 12,579 (89.60%)
phastCons 14,197 10,217 (71.97%) 100.64 0.21 3.79 11,018 (77.60%) 324.41 0.14 5.76 11,116 (78.29%)
phyloP 14,202 9910 (69.78%) 118.81 0.40 3.31 10,107 (71.17%) 332.05 0.31 7.15 10,131 (71.34%)
Polyphen2_HDIV 14,745 11,824 (80.19%) 65.48 0.14 4.89 12,558 (85.16%) 257.00 0.12 12.08 12,658 (85.84%)
Polyphen2_HVAR 14,741 11,470 (77.81%) 59.67 0.11 5.47 12,621 (85.62%) 239.71 0.09 14.03 12,778 (86.69%)
PROVEAN 13,888 9733 (70.08%) 74.16 0.23 3.37 9958 (71.70%) 219.39 0.17 7.93 10,003 (72.02%)
SIFT 14,561 11,088 (76.15%) 99.69 0.25 3.69 11,224 (77.08%) 265.64 0.20 7.04 11,257 (77.31%)
VEST3 14,170 9919 (70.00%) 53.36 0.09 5.69 10,528 (74.29%) 136.56 0.08 12.56 10,821 (76.36%)
  1. aAcross the cohort of 508 individuals assessed, individual samples have a very high median number of invariant genes resulting on GenePy scores of zero