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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).