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Table 2 Summary of huvariome genomes

From: Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection

Description

Female (range)

Male (range)

All (range)

Gross mapping yield (Gb)

206 (160–280)

202 (168–249)

206 (160–280)

Fully called genome fraction

95.13% (91%/97%)

95.89% (94%/97%)

95.13% (91%/97%)

Partially called genome fraction

0.96% (0%/2%)

0.69% (0%/1%)

0.96% (0%/2%)

No-called genome fraction

3.91% (3%/7%)

3.42% (2%/5%)

3.91% (2%/7%)

SNP total count

3257897 (2966002–3396520)

3275018 (3056972–3495143)

3257897 (2966002–3495143)

SNP novel rate

6.71% (6%/7%)

6.78% (6%/9%)

6.71% (6%/9%)

 Synonymous SNP

9239 (8668–9564)

9229 (8503–9821)

9239 (8503–9821)

 Missense SNP

9046 (8348–9456)

9037 (8380–9574)

9046 (8348–9574)

 Nonsense SNP

96 (86–117)

95 (77–110)

96 (77–117)

 Nonstop SNP

24 (19–29)

22 (17–26)

24 (17–29)

INS total count

180040 (152082–208451)

190177 (160473–209226)

180040 (152082–209226)

INS novel rate

21.31% (19%/23%)

21.58% (19%/23%)

21.31% (19%/23%)

 Frame-shifting INS

134 (113–157)

130 (95–152)

134 (95–157)

 Frame-preserving INS

116 (96–132)

117 (98–130)

116 (96–132)

DEL total count

192550 (157937–217782)

202085 (166805–227228)

192550 (157937–227228)

DEL novel rate

23.85% (23%/25%)

23.75% (22%/26%)

23.85% (22%/26%)

 Frame-shifting DEL

117 (96–144)

110 (86–126)

117 (86–144)

 Frame-preserving DEL

120 (100–138)

115 (106–128)

120 (100–138)

SUB total count

68020 (56179–75040)

69396 (59319–76699)

68020 (56179–76699)

SUB novel rate

34.07% (31%/38%)

33.96% (31%/37%)

34.07% (31%/38%)

 Frame-shifting SUB

21 (11–27)

19 (14–26)

21 (11–27)

 Frame-preserving SUB

259 (208–320)

252 (225–279)

259 (208–320)

  1. The data represent the average counts from the 31 genomes of Huvariome Core in which the fraction of heterozygous SNPs, inserts, deletions or substitutions are not found in dbSNP (SNP, INS, DEL, SUB novel). The number of loci where a coding SNV did not result in protein sequence change (Synonymous SNP), number of loci where a coding SNV resulted in protein sequence change, with no change in size of protein (Missense SNP), number of loci where the single nucleotide change in coding sequence resulted in a STOP codon (TGA, TAG, or TAA), causing an early termination of protein translation (Nonsense SNP), number of loci where the single nucleotide change in coding sequence resulted in the change of a STOP codon into a codon that codes for an amino acid, resulting in the continuation of the translation for this protein (Nonstop SNP), number of loci where the single nucleotide change in coding sequence resulted in the change of a START codon into a codon for something other than a start codon, likely resulting in a non-functional gene (Misstart SNP). The number of insertion, deletion or substitution loci where the change in coding sequence resulted in a frameshift for the encoded protein (Frame-shifting INS, DEL, SUB), number loci where there is a change in coding sequence and the length of the insertion is a multiple of 3, resulting in the insertion of amino acids in the encoded protein in-frame (Frame-preserving INS, DEL, SUB).
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Journal of Clinical Bioinformatics

ISSN: 2043-9113