Table 2 Mean shares (%) of the eight categories of haplotypes identified by the KDE-based local classification, in each population and subpopulation of the Asian and Malagasy diversity panels

Asian Panel

indica

68.9

1.2

0.9

4.8

12.3

2.9

8.9

0.1

(59.8–84.8)

(0.9–1.9)

(0.4–2.7)

(2.1–7.4)

(5.8–19.2)

(1.6–4.5)

(3.8–15.7)

(0–0.4)

- XI-1

67.6

0.5

1.0

5.2

12.4

3.4

9.8

0.1

(57.6–85.6)

(0.2–1.6)

(0.3–2.9)

(2–7.9)

(4.3–17.9)

(1.7–9)

(4.1–18.9)

(0–0.2)

- XI-2

65.6

2.9

0.5

4.4

14.5

2.8

8.5

0.8

(51.4–80)

(1.9–4.8)

(0.2–1.6)

(1.7–6.6)

(8.4–23.2)

(−0.4–4.7)

(1.2–15.1)

(0–8.6)

- XI-3

72.7

0.3

0.5

4.6

10.9

2.7

8.3

0.1

(60.8–88.5)

(0.1–0.7)

(0.1–2.4)

(2–9.3)

(4.1–19.9)

(1.5–4.5)

(3.3–13.9)

(0–0.3)

- X-adm

67.2

1.5

1.4

5.0

12.6

3.0

9.2

0.1

(57.5–83.5)

(1.2–2.3)

(0.7–3.3)

(2.2–7.2)

(6.2–18.9)

(1.7–4.6)

(4.1–16.1)

(0–0.5)

japonica

1.0

0.4

58.4

13.8

3.8

4.0

17.7

0.8

(0.4–1.8)

(0.3–0.7)

(36.4–71.6)

(3–23.2)

(2.7–6.5)

(2.7–6.5)

(9.7–27.3)

(0.1–7.2)

- GJ-trop

1.1

0.5

58.2

14.7

3.7

3.9

16.0

2.0

(0.3–2.0)

(0.3–1.1)

(36.3–71.9)

(3.1–23.2)

(1.9–6.4)

(1.8–6.3)

(8.4–27.4)

(0.1–9.8)

- GJ-sbtrop

0.8

0.4

58.4

14.5

4.1

4.2

16.5

1.3

(0.1–1.7)

(0.1–0.9)

(40.9–73.4)

(2.9–23.9)

(2.8–6.9)

(2.8–6.4)

(9.1–25.5)

(0.1–6.6)

- GJ-temp

1.0

0.2

55.7

14.6

4.5

4.6

18.2

0.8

(0.4–2.4)

(0.0–0.6)

(33.7–71.4)

(3.2–23.0)

(2.8–6.9)

(2.9–7.1)

(11.1–28.1)

(0.0–3.9)

- GJ-adm

2.7

0.7

54.8

14.8

4.4

4.4

17.1

1.5

(1.4–5.0)

(0.3–1.1)

(35.3–70.3)

(5.1–22.7)

(3.0–6.5)

(2.8–6.6)

(9.8–27.9)

(0.0–6.6)

cAus

1.8

53.1

0.8

3.3

26.4

3.5

10.8

0.2

(1.3–2.3)

(37.6–63.8)

(0.5–2)

(1.7–6.7)

(14.4–42.2)

(1.8–6.7)

(4.8–18.4)

(0–0.4)

cBas

16.9

13.2

31.2

6.9

7.1

2.6

11.1

11.0

(10.6–27.4)

(4.9–22.4)

(20.7–38.7)

(2.2–12.9)

(2.9–10.9)

(−0.9–5.4)

(4.4–21.2)

(6.1–23.7)

Admix

24.4

12.4

24.3

7.4

10.6

4.3

10.3

6.2

(20.1–27.2)

(8.7–16.4)

(16.4–30.9)

(2.3–11.3)

(7.5–14.5)

(2–13.3)

(1.8–17.2)

(4.9–9.7)

Malagasy panel

G1

69.7

1.3

0.6

5.0

11.9

2.8

8.4

0.4

(59.9–84.2)

(0.6–2.3)

(0.1–2.1)

(2.0–7.6)

(4.5–17)

(1.6–4.2)

(3–16.2)

(0.1–1.2)

G6

2.7

2.0

57.4

12.5

3.9

3.8

15.0

3.1

(1.5–4.8)

(0.8–4.1)

(38.3–69.0)

(3.0–18.9)

(2–7)

(1.6–6.8)

(7.1–23.1)

(1.2–10.8)

Gm

50.6

8.2

5.4

5.7

14.3

3.3

9.8

2.6

(34.9–79.6)

(2.4–19.8)

(1.2–24)

(2.1–13.2)

(6–21.5)

(1.8–6.3)

(3.7–19.2)

(1.3–3.8)

Admix

58.9

6.2

3.4

4.6

12.5

2.8

7.4

4.1

(49.2–75.0)

(2.4–8.3)

(2.6–5.1)

(1.9–8.8)

(5.0–20.5)

(1.0–5.2)

(1.6–12.9)

(2.3–6.2)