Table 1 Median autosomal variant sites per genome

From: A global reference for human genetic variation

  AFR AMR EAS EUR SAS
Samples 661 347 504 503 489
Mean coverage 8.2 7.6 7.7 7.4 8.0
  Var. sites Singletons Var. sites Singletons Var. sites Singletons Var. sites Singletons Var. sites Singletons
SNPs 4.31M 14.5k 3.64M 12.0k 3.55M 14.8k 3.53M 11.4k 3.60M 14.4k
Indels 625k - 557k - 546k - 546k - 556k -
Large deletions 1.1k 5 949 5 940 7 939 5 947 5
CNVs 170 1 153 1 158 1 157 1 165 1
MEI (Alu) 1.03k 0 845 0 899 1 919 0 889 0
MEI (L1) 138 0 118 0 130 0 123 0 123 0
MEI (SVA) 52 0 44 0 56 0 53 0 44 0
MEI (MT) 5 0 5 0 4 0 4 0 4 0
Inversions 12 0 9 0 10 0 9 0 11 0
Nonsynon 12.2k 139 10.4k 121 10.2k 144 10.2k 116 10.3k 144
Synon 13.8k 78 11.4k 67 11.2k 79 11.2k 59 11.4k 78
Intron 2.06M 7.33k 1.72M 6.12k 1.68M 7.39k 1.68M 5.68k 1.72M 7.20k
UTR 37.2k 168 30.8k 136 30.0k 169 30.0k 129 30.7k 168
Promoter 102k 430 84.3k 332 81.6k 425 82.2k 336 84.0k 430
Insulator 70.9k 248 59.0k 199 57.7k 252 57.7k 189 59.1k 243
Enhancer 354k 1.32k 295k 1.05k 289k 1.34k 288k 1.02k 295k 1.31k
TFBSs 927 4 759 3 748 4 749 3 765 3
Filtered LoF 182 4 152 3 153 4 149 3 151 3
HGMD-DM 20 0 18 0 16 1 18 2 16 0
GWAS 2.00k 0 2.07k 0 1.99k 0 2.08k 0 2.06k 0
ClinVar 28 0 30 1 24 0 29 1 27 1
  1. See Supplementary Table 1 for continental population groupings. CNVs, copy-number variants; HGMD-DM, Human Gene Mutation Database disease mutations; k, thousand; LoF, loss-of-function; M, million; MEI, mobile element insertions.