a ChinaMAP

ChinaMAP & dbSNP

b
AF > 5% 2.14% Log10 (number of INDELs)
ChinaMAP & 1KGP
ChinaMAP & gnomAD
ChinaMAP & TOPMed AF = 0
AF ≤ 5% 4.28% ChinaMAP & dbSNP & 1KGP 7

Frequency of TOPMed
ChinaMAP & dbSNP & gnomAD
ChinaMAP & dbSNP & TOPMed AF ≤ 0.01%
ChinaMAP & 1KGP & gnomAD
AF ≤ 1% 10.26% ChinaMAP & 1KGP & TOPMed 6
ChinaMAP & gnomAD & TOPMed AF ≤ 0.1%
ChinaMAP & dbSNP & 1KGP & gnomAD
AF ≤ 0.1% 28.51% ChinaMAP & dbSNP & 1KGP & TOPMed
ChinaMAP & dbSNP & gnomAD & TOPMed AF ≤ 1% 5
ChinaMAP & 1KGP & gnomAD & TOPMed
ChinaMAP & dbSNP & 1KGP & gnomAD & TOPMed
AC = 2 58.34% AF ≤ 5%
4

AC = 1 76.00% AF > 5%

AF = 0 AF ≤ 0.01%AF ≤ 0.1% AF ≤ 1% AF ≤ 5% AF > 5%

0 20 40 60
Number of INDELs (×100K) Frequency of ChinaMAP
c d
Log10 (number of SNPs) Log10 (number of INDELs)

7 7
AF = 0 AF = 0
Frequency of gnomAD

Frequency of gnomAD
AF ≤ 0.01% 6 6
AF ≤ 0.01%

AF ≤ 0.1% 5 AF ≤ 0.1%
5
AF ≤ 1%
AF ≤ 1%
4 4
AF ≤ 5% AF ≤ 5%
3 3
AF > 5% AF > 5%
AF = 0 AF ≤ 0.01% AF ≤ 0.1% AF ≤ 1% AF ≤ 5% AF > 5% AF = 0 AF ≤ 0.01% AF ≤ 0.1% AF ≤ 1% AF ≤ 5% AF > 5%
Frequency of ChinaMAP Frequency of ChinaMAP

e
Province: Shanghai (1,910) Anhui (70) Shandong (481) Liaoning (319) Shanxi (75) Henan (163) Guangdong (919) Sichuan (456) Xizang (137)
Jiangsu (213) Fujian (959) Heilongjiang (31) Beijing (61) Hebei (317) Hubei (1,090) Guangxi (96) Guizhou (390) Shaanxi (92)
Zhejiang (1,413) Jiangxi (45) Jilin (40) Tianjin (72) Neimenggu (273) Hunan (375) Chongqing (21) Yunnan (11) Gansu (559)
3.75
Number of INDELs (×100K)

3.65

3.55

3.45

3.35
East China Northeast China North China Central China South China Southwest China Northwest China

f
Ethnic group: Han (9,043) Hui (222) Manchu (208) Miao (245) Mongolian (228) Tibetan (207) Yi (212) Zhuang (223)

3.55 3.75
Number of INDELs (×100K)
Number of SNPs (×1M)

3.45 3.65

3.35 3.55

3.25 3.45

3.15 3.35
Ethnic group Ethnic group
Fig. S2 Analysis and statistics of autosomal INDELs. a The number and allele

frequency spectrum of known and novel autosomal INDELs identified in the

ChinaMAP compared with the TOPMed, gnomAD, dbSNP and 1KGP database. b

The frequency distribution of INDELs between the ChinaMAP and TOPMed. c, d

The frequency distribution of autosomal SNPs and INDELs between the ChinaMAP

and gnomAD. e The number of autosomal INDELs identified in different provinces

and geographical divisions of China. f The number of autosomal SNPs and INDELs

identified in ethnic groups.