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Table 1 Summary of data sets included in PGG.SNV

From: PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations

Data set Abbr. Data set Type Ancient (Archaic) No. Genomes No. Populations (Ancestries) References
NHLBI Exome Sequencing Project ESP EGS N 6503 2 [3]
Genome of the Netherlands GoNL WGS N 769 1 [42]
Whole-genome sequences of 3554 healthy Japanese individuals 3.5KJPN WGS N 3554 1 [43]
Genome Aggregation Database gnomAD.genomes and gnomAD.exomes WGS and EGS N 141,456 25 [39]
1000 genomes project phase 3 1KG_phase3 WGS N 2504 26 [4]
Estonian Biocentre data set Estonian_Biocentre Genotyping N 1297 123 [44,45,46,47,48,49,50,51,52,53]
Human Origins data set HuOrigin Genotyping N 2327 202 [54]
Simons Genome Diversity Project SGDP WGS N 261 128 [6]
Human Genome Diversity Project HGDP Genotyping N 937 53 [2]
International HapMap Project HapMap Genotyping N 1397 11 [1]
Asian Genome Diversity Project AGDP Genotyping N 3605 40 [55]
Negrito Pygmy data set NegPyg Genotyping N 1233 61 [56,57,58,59,60,61]
Pan-Asian SNP Consortium PASNP Genotyping N 1691 71 [62]
Asian Admixed Genomes Consortium AAGC WGS N 1009 16
Han Chinese Genomes Project HanGenomesProject Genotyping N 51,094 38
Singapore Genome Variation Project SGVP WGS N 132 2 [63, 64]
Indian genomes Indian Genomes Genotyping N 378 52 [65]
The complete genome sequence of a Neanderthal from the Altai Mountains AltaiNea WGS Y 1 1 [66]
A High-Coverage Genome Sequence from an Archaic Denisovan Individual DenisovaPinky WGS Y 1 1 [67]
Genome sequence of a 45,000-year-old modern human from western Siberia. Ust_Ishim WGS Y 1 1 [68]
Ancient anatomically modern humans AAMH GWADD Y 989 109 [69,70,71,72,73,74,75]
Ancient anatomically modern humans (Southeast Asians) AAMH.SoutheastAsia WGS Y 26 13 [76]
  1. Ancient individuals from the same country and same age period are grouped into one ancient population. N no, Y yes, EGS exome genome sequencing, WGS whole-genome sequencing, GWADD genome-wide ancient DNA dataset, No. number of, Abbr abbreviation; “–”, unpublished