SNP Profiles of ICS 40 View Data

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	1	2	3	4	5	6	7	8	9	10	11	12	13	14
_Input profile	CT	AG	GG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
1._ICS_40	__	__	GG	CT	TT	AA	__	GT	CT	CT	AA	AA	CT	AA
2._ICS_40	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
3._GC-01-106-6-03	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
4._GC-01-106-6-03	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
5._GC-01-106-6-03	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
6._GC-01-106-6-03	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
7._ICS_40	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
8._ICS_40	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
9._ICS_40	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
10._ICS_40	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
11._GC-01-106-6-03	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
12._RUQ_1432	CT	AG	CG	CT	CT	AA	CC	GT	CT	CT	AA	AA	CT	AA
13._GC-01-106-6-03	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
14._GC-01-106-6-03	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
15._GC-01-106-6-03	CT	AG	CG	CT	TT	AA	CC	__	CT	CT	AA	AA	CT	AA
16._ICS_40	CT	AG	CG	CT	TT	AA	CC	__	CT	CT	AA	AA	CT	AA
17._ICS_40	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
18._ICS_40	CT	AG	CG	CT	TT	AA	CC	GT	CT	CT	AA	AA	CT	AA
19._RUQ_1432	__	__	CG	__	__	__	__	GT	__	CT	__	AA	__	AA
20._RUQ_1432	__	AG	CG	CT	__	__	__	GT	__	__	__	__	CT	AA
21._ICS_40	CC	GG	GG	TT	CT	AC	CT	GT	CC	CC	AA	GG	CC	AA
22._GC-01-106-6-03	CC	GG	CC	TT	CT	AC	CT	GG	TT	CC	AA	GG	CC	AA
23._ICS_40	CC	GG	CC	TT	CT	AC	CT	GG	TT	CC	AA	GG	CC	AA
24._RUQ_1432	AG	AG	CC	AG	AA	AA	GG	AA	__	__	AA	AA	AG	AA

	15	16	17	18	19	20	21	22	23	24	25	26	27	28
_Input profile	CT	AA	GG	TT	CC	CG	GT	AG	CT	AC	CC	GT	CT	CC
1._ICS_40	CT	AA	GG	TT	CC	CG	GT	AG	CT	__	CC	GT	CT	CC
2._ICS_40	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
3._GC-01-106-6-03	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
4._GC-01-106-6-03	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
5._GC-01-106-6-03	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
6._GC-01-106-6-03	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
7._ICS_40	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
8._ICS_40	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
9._ICS_40	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
10._ICS_40	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
11._GC-01-106-6-03	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
12._RUQ_1432	CT	AA	GG	TT	CC	CG	GT	AG	CT	AC	CC	GT	CT	CC
13._GC-01-106-6-03	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
14._GC-01-106-6-03	__	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
15._GC-01-106-6-03	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
16._ICS_40	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
17._ICS_40	__	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
18._ICS_40	CT	AA	GG	TT	CC	CG	GT	GG	CT	AC	CC	GT	CT	CC
19._RUQ_1432	__	__	__	__	__	CG	GT	AG	__	AC	CC	__	__	CC
20._RUQ_1432	__	__	__	__	CC	CG	GT	__	CT	AA	CC	GT	CT	CC
21._ICS_40	CT	AA	CG	CT	CC	CG	GG	AA	CT	CC	CC	TT	CT	AC
22._GC-01-106-6-03	CT	AT	GG	CT	TT	CC	GT	AA	TT	CC	GG	GG	CC	AA
23._ICS_40	CT	AT	GG	CT	TT	CC	GT	AA	TT	CC	GG	GG	CC	AA
24._RUQ_1432	AG	AA	GG	AA	GG	CG	AC	__	AG	AC	CC	AC	__	CC

	29	30	31	32	33	34	35	36	37	38	39	40
_Input profile	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
1._ICS_40	AG	GG	__	CT	AG	__	AC	__	GT	AC	AT	GG	X_X	X_X
2._ICS_40	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
3._GC-01-106-6-03	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
4._GC-01-106-6-03	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
5._GC-01-106-6-03	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
6._GC-01-106-6-03	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
7._ICS_40	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
8._ICS_40	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
9._ICS_40	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
10._ICS_40	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
11._GC-01-106-6-03	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
12._RUQ_1432	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
13._GC-01-106-6-03	AG	GG	AT	CT	AG	CG	__	CT	GT	AC	AT	GG	X_X	X_X
14._GC-01-106-6-03	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
15._GC-01-106-6-03	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
16._ICS_40	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
17._ICS_40	AG	GG	AT	CT	AG	CG	AC	CT	GT	AC	AT	GG	X_X	X_X
18._ICS_40	AG	GG	AT	CT	AG	CG	__	CT	GT	AC	AT	GG	X_X	X_X
19._RUQ_1432	__	__	__	__	AG	__	__	__	__	AC	__	__	X_X	X_X
20._RUQ_1432	AG	__	AT	CT	AG	CG	AC	CT	GT	AC	__	__	X_X	X_X
21._ICS_40	AA	AG	AA	TT	AA	GG	AC	CC	GT	CC	TT	CG	X_X	X_X
22._GC-01-106-6-03	AG	AA	AT	CC	AG	CC	CC	TT	GG	AC	AT	GG	X_X	X_X
23._ICS_40	AG	AA	AT	CC	AG	CC	CC	TT	GG	AC	AT	GG	X_X	X_X
24._RUQ_1432	__	GG	AT	AG	AG	CG	AC	AG	AC	AC	AT	GG	X_X	X_X

Input profile: ICS_40

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Malaysian Cocoa Board (MCB), Malaysia

Location: C0201 2A

Dapeng Zhang, 2016

1._ICS_40

identical
33 shared markers

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International Cocoa Genebank, Trinidad (ICG,T), Trinidad and Tobago

Location: San Juan Block2

Dapeng Zhang, 2016

2._ICS_40

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 4

Dapeng Zhang, 2016

3._ICS_40 GC-01-106-6-03

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 4

Notes: Dead

4._ICS_40 GC-01-106-6-03

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 1

Notes: 1

5._ICS_40 GC-01-106-6-03

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 6

Notes: Dead

6._ICS_40 GC-01-106-6-03

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 11

Notes: 11

7._ICS_40

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 1

Dapeng Zhang, 2016

8._ICS_40

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 6

Dapeng Zhang, 2016

9._ICS_40

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 11

Dapeng Zhang, 2016

10._ICS_40

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 13

Dapeng Zhang, 2016

11._ICS_40 GC-01-106-6-03

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 13

Notes: 13

12._ICS_40 RUQ_1432

97.5 %
40 shared markers

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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom

Dapeng Zhang, 2016

13._ICS_40 GC-01-106-6-03

97.4 %
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Field: 1, Block: 6, Rep: 3, Tree: PL6

Notes: PL6 FP4

14._ICS_40 GC-01-106-6-03

97.4 %
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Field: 1, Block: 6, Rep: 3, Tree: PL4

Notes: PL4 FP3

15._ICS_40 GC-01-106-6-03

97.4 %
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 16

Notes: 16

16._ICS_40

97.4 %
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 16

Dapeng Zhang, 2016

17._ICS_40

97.4 %
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 4 > FP

Dapeng Zhang, 2016

18._ICS_40

97.4 %
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 6 > FP

Dapeng Zhang, 2016

19._ICS_40 RUQ_1432

96.2 %
13 shared markers

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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom

Lambert Motilal, 2023

Population Assignment:

Ame
0.489 Cri
0.505

20._ICS_40 RUQ_1432

95.8 %
24 shared markers

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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom

Dapeng Zhang, 2014

21._ICS_40

65 %
40 shared markers

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International Cocoa Genebank, Trinidad (ICG,T), Trinidad and Tobago

Location: 6B E287 T4

Dapeng Zhang, 2016

22._ICS_40 GC-01-106-6-03

56.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 9

Notes: 9

23._ICS_40

56.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 1603 9

Dapeng Zhang, 2016

24._ICS_40 RUQ_1432

54.3 %
35 shared markers

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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom

Notes: Reading_Collection

Key to SNP Markers

Key to SNP Markers

1	TcSNP1520	2	TcSNP1484	3	TcSNP1458	4	TcSNP1442	5	TcSNP1414
6	TcSNP1350	7	TcSNP1270	8	TcSNP1253	9	TcSNP1165	10	TcSNP1144
11	TcSNP1075	12	TcSNP1062	13	TcSNP1060	14	TcSNP998	15	TcSNP994
16	TcSNP953	17	TcSNP929	18	TcSNP917	19	TcSNP891	20	TcSNP872
21	TcSNP723	22	TcSNP645	23	TcSNP619	24	TcSNP591	25	TcSNP577
26	TcSNP560	27	TcSNP534	28	TcSNP529	29	TcSNP469	30	TcSNP429
31	TcSNP372	32	TcSNP242	33	TcSNP230	34	TcSNP226	35	TcSNP193
36	TcSNP151	37	TcSNP150	38	TcSNP144	39	TcSNP32	40	TcSNP25