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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sequencing, WGS whole-genome sequencing, GWADD genome-wide ancient DNA dataset, No. number of, Abbr abbreviation; “–”, unpublished
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Genome Biology

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