SNP Profiles matching SGU 54

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	1	2	3	4	5	6	7	8	9	10	11	12	13	14
_Input profile	GG	TT	CC	GT	CT	AC	CG	AG	CT	AA	GG	AG	CC	CT
1._RUQ_909	_	_	CC	GT	CT	AC	CG	AG	CT	AT	_	AG	CC	CT
2._RUQ_909	_	_	CC	GT	CT	AC	CG	AG	CT	AT	_	AG	CC	CT
3._CC_10	GG	TT	CC	GT	_	AC	_	AG	CT	_	GG	AG	CC	CT
4._CC_10	GG	TT	CC	GT	CT	AC	CG	AG	CT	AT	GG	AG	CC	CT
5._CC_10	GG	TT	CC	GT	CT	AC	CG	AG	CT	AT	GG	AG	CC	CT
6._CC_10	GG	TT	CC	GT	CT	AC	CG	AG	CT	AT	GG	AG	CC	CT
7._CC_10	GG	TT	CC	GT	CT	AC	CG	AG	CT	AT	GG	AG	CC	CT
8._GC-08-271-8-43	GG	TT	CC	GT	CT	AC	CG	AG	CT	AT	GG	AG	CC	CT
9._GC-08-271-8-43	GG	TT	CC	GT	CT	AC	CG	AG	CT	AT	GG	AG	CC	CT
10._GC-08-271-8-43	GG	TT	CC	GT	CT	AC	CG	AG	CT	AT	GG	AG	CC	CT
11._GC-08-271-8-43	GG	TT	CC	GT	CT	AC	CG	AG	CT	AT	GG	AG	CC	CT
12._UF_668	GG	AT	AC	GT	_	AC	_	AG	CT	_	GG	_	CC	CT
13._CC_10	GG	TT	CC	GT	CT	AC	CG	AG	_	AT	GG	AG	CC	CT
14._GC-08-271-8-43	GG	TT	CC	GT	CT	AC	CG	AG	_	AT	GG	AG	CC	CT
15._MARPER_45	-	AT	-	GT	-	-	-	AG	CT	-	GG	AG	CC	TT
16._CC_10	GG	TT	CC	GT	CT	AC	CG	AG	CT	TT	GG	AG	CC	CT

	15	16	17	18	19	20	21	22	23	24	25	26	27	28
_Input profile	TT	CC	AC	TT	AG	GT	GG	CC	TT	GG	AA	TT	AG	CC
1._RUQ_909	GT	CC	CC	TT	_	GT	GG	CC	_	_	_	_	AG	CC
2._RUQ_909	GT	CC	CC	TT	_	GT	GG	CC	_	_	_	_	AG	CC
3._CC_10	TT	CC	_	CT	AG	GT	GG	CC	TT	GG	AA	CT	AG	CT
4._CC_10	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
5._CC_10	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
6._CC_10	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
7._CC_10	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
8._GC-08-271-8-43	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
9._GC-08-271-8-43	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
10._GC-08-271-8-43	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
11._GC-08-271-8-43	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
12._UF_668	_	CC	_	CT	AG	GT	CG	CC	TT	GG	_	CT	_	_
13._CC_10	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
14._GC-08-271-8-43	TT	CC	AC	CT	GG	GT	GG	CC	TT	GG	AA	CT	AG	CT
15._MARPER_45	-	CC	-	TT	GG	GT	-	CC	-	GG	AA	TT	AG	-
16._CC_10	TT	CC	AC	CT	AG	GT	GG	CC	TT	GG	AA	CT	AG	CT

	29	30	31	32	33	34	35	36	37	38	39	40
_Input profile	AA	AA	TT	CT	GT	CC	AA	TT	CT	CG	AA	CT	X_X	X_X
1._RUQ_909	_	_	_	_	GT	_	_	_	CT	CG	AA	_	X_X	X_X
2._RUQ_909	_	_	_	_	GT	_	_	_	CT	CG	AA	_	X_X	X_X
3._CC_10	AA	AA	CT	CT	GT	_	AA	TT	CT	GG	_	_	X_X	X_X
4._CC_10	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
5._CC_10	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
6._CC_10	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
7._CC_10	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
8._GC-08-271-8-43	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
9._GC-08-271-8-43	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
10._GC-08-271-8-43	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
11._GC-08-271-8-43	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
12._UF_668	AA	AA	_	CT	GT	CC	AA	TT	CT	CG	_	_	X_X	X_X
13._CC_10	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
14._GC-08-271-8-43	AA	AA	CT	CT	GT	CC	AA	TT	CT	CG	AG	CT	X_X	X_X
15._MARPER_45	AA	AA	-	CT	-	CC	AA	-	CT	GG	AA	TT	X_X	X_X
16._CC_10	AA	AA	CT	CT	GT	CC	AA	TT	CT	GG	AG	CT	X_X	X_X

Input profile: SGU_54

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

Location: Cabiria

Dapeng Zhang, 2016

1._CRU_124 RUQ_909

93.8 %
24 shared markers

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

Dapeng Zhang, 2014

2._CRU_124 RUQ_909

93.8 %
24 shared markers

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

Dapeng Zhang, 2014

3._CC_10

92.4 %
33 shared markers

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

Location: Cabiria

Dapeng Zhang, 2016

4._CC_10

91.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8843 9

Dapeng Zhang, 2016

5._CC_10

91.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8843 7

Dapeng Zhang, 2016

6._CC_10

91.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8843 5

Dapeng Zhang, 2016

7._CC_10

91.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8843 1

Dapeng Zhang, 2016

Population Assignment:

Dapeng Zhang, 2016

8._CC_10 GC-08-271-8-43

91.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 1

Notes: 1

9._CC_10 GC-08-271-8-43

91.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 5

Notes: 5

10._CC_10 GC-08-271-8-43

91.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 7

Notes: Dead

11._CC_10 GC-08-271-8-43

91.3 %
40 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 9

Notes: Dead

12._UF_668

91.1 %
28 shared markers

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

Location: La Montaña Lot 8 Row 27 31_33

Dapeng Zhang, 2016

13._CC_10

91 %
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8843 2

Dapeng Zhang, 2016

14._CC_10 GC-08-271-8-43

91 %
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 2

Notes: 2

15._MARPER_45

90.4 %
26 shared markers

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

Location: MARPER D 251A

Dapeng Zhang, 2014

16._CC_10

90 %
40 shared markers

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Malaysian Cocoa Board (MCB), Malaysia

Location: Trial 1/Rep 1 45

Dapeng Zhang, 2016

Key to SNP Markers

Key to SNP Markers

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