SNP Profiles matching LF 1

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	1	2	3	4	5	6	7	8	9	10	11	12	13	14
_Input profile	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
1._LF_1	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
2._LF_1	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
3._LF_1	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
4._GC-08-285-8-57	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
5._GC-08-285-8-57	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
6._GC-08-285-8-57	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
7._GC-08-285-8-57	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
8._LF_1	CC	GG	CC	TT	TT	AA	CC	GG	CT	CC	AA	AA	CT	AG
9._RUQ_17	_	GG	CC	TT	_	_	_	-	_	_	_	_	CT	AG
10._CCN_51	CC	GG	CC	TT	TT	AA	CC	GG	TT	CC	AA	AA	TT	AA

	15	16	17	18	19	20	21	22	23	24	25	26	27	28
_Input profile	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
1._LF_1	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
2._LF_1	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
3._LF_1	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
4._GC-08-285-8-57	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
5._GC-08-285-8-57	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
6._GC-08-285-8-57	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
7._GC-08-285-8-57	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
8._LF_1	CT	AA	GG	TT	CC	CC	TT	CT	CC	CC	GG	CC	CC	GG
9._RUQ_17	_	_	_	_	-	CC	TT	CT	CC	-	GG	CC	CC	GG
10._CCN_51	CC	AA	GG	TT	CC	CC	TT	CC	CC	CC	GG	CC	CC	GG

	29	30	31	32	33	34	35	36	37	38	39
_Input profile	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
1._LF_1	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
2._LF_1	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
3._LF_1	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
4._GC-08-285-8-57	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
5._GC-08-285-8-57	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
6._GC-08-285-8-57	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
7._GC-08-285-8-57	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
8._LF_1	GG	TT	TT	GG	GG	CC	CT	GT	AA	AA	GG	X_X	X_X	X_X
9._RUQ_17	_	TT	TT	GG	GG	CC	CT	GT	AA	_	_	X_X	X_X	X_X
10._CCN_51	GG	TT	TT	GG	GG	CC	TT	GG	AA	AA	GG	X_X	X_X	X_X

Input profile: LF_1

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Mars Center for Cocoa Science, Brazil

Location: 8857 4

Dapeng Zhang, 2016

1._LF_1

identical
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8857 8

Dapeng Zhang, 2016

2._LF_1

identical
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8857 7

Dapeng Zhang, 2016

3._LF_1

identical
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8857 2

Dapeng Zhang, 2016

Population Assignment:

Dapeng Zhang, 2016

4._LF_1 GC-08-285-8-57

identical
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 2

Notes: 2

5._LF_1 GC-08-285-8-57

identical
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 4

Notes: 4

6._LF_1 GC-08-285-8-57

identical
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 7

Notes: 7

7._LF_1 GC-08-285-8-57

identical
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 8

Notes: 8

8._LF_1

identical
39 shared markers

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Malaysian Cocoa Board (MCB), Malaysia

Location: C0298

Dapeng Zhang, 2016

9._LF_1 RUQ_17

identical
21 shared markers

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

Dapeng Zhang, 2014

10._CCN_51

91 %
39 shared markers

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Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Costa Rica

Location: Cabiria

Dapeng Zhang, 2016

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	TcSNP619	23	TcSNP591	24	TcSNP577	25	TcSNP560
26	TcSNP534	27	TcSNP529	28	TcSNP469	29	TcSNP429	30	TcSNP372
31	TcSNP242	32	TcSNP230	33	TcSNP226	34	TcSNP193	35	TcSNP151
36	TcSNP150	37	TcSNP144	38	TcSNP32	39	TcSNP25