Skip to main content

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
Back to article page

BMC Bioinformatics

ISSN: 1471-2105

Contact us