SNP Profiles matching SPEC 160/9

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	1	2	3	4	5	6	7	8	9	10	11	12	13	14
_Input profile	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
1._RUQ_51	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
2._RUQ_51	_	_	AC	GT	CT	AC	CG	AG	CT	AT	_	CC	CT	CC
3._ICS_40	GG	AT	AC	GT	_	AC	_	AG	CT	_	GG	CC	CT	CC
4._SPEC_160_/9	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
5._SPEC_160_/9	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
6._SPEC_160_/9	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
7._SPEC_160_/9	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
8._SPEC_160_/9	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
9._GC-08-267-8-39	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
10._GC-08-267-8-39	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
11._GC-08-267-8-39	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
12._GC-08-267-8-39	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
13._GC-08-267-8-39	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
14._UF_668	GG	AT	AC	GT	_	AC	_	AG	CT	_	GG	CC	CT	CC
15._UF_12	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
16._UF_668	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
17._ICS_60	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CG
18._UF_676	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
19._ICS_39	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
20._ICS_40	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
21._ICS_60	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CG
22._UF_12	GG	AT	AC	GT	CT	AC	CG	AG	CT	AT	GG	CC	CT	CC
23._ICS_60	GG	AT	AC	GT	CT	_	CG	AG	CT	AT	GG	CC	CT	CG
24._RUQ_54	_	_	AC	GT	CT	AC	CG	AG	CT	AT	_	CC	CT	CC

	15	16	17	18	19	20	21	22	23	24	25	26	27	28
_Input profile	AT	CC	AG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
1._RUQ_51	AC	CC	AG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
2._RUQ_51	AA	CC	_	GT	CG	CC	_	_	_	_	_	_	GG	_
3._ICS_40	_	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GT	_
4._SPEC_160_/9	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
5._SPEC_160_/9	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
6._SPEC_160_/9	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
7._SPEC_160_/9	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
8._SPEC_160_/9	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
9._GC-08-267-8-39	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
10._GC-08-267-8-39	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
11._GC-08-267-8-39	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
12._GC-08-267-8-39	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
13._GC-08-267-8-39	AC	CC	GG	GT	CG	CC	TT	GG	CC	AA	AA	CT	GG	CC
14._UF_668	_	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GT	CC
15._UF_12	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GT	CC
16._UF_668	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GT	CC
17._ICS_60	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GG	CC
18._UF_676	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GT	CC
19._ICS_39	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GT	CC
20._ICS_40	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GT	CC
21._ICS_60	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GG	CC
22._UF_12	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GT	CC
23._ICS_60	AC	CT	AG	GT	CG	CC	TT	GG	CT	AA	AA	CT	GG	CC
24._RUQ_54	AA	CT	_	GT	CG	CC	_	_	_	_	_	_	GT	_

	29	30	31	32	33
_Input profile	AA	TT	CT	GG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
1._RUQ_51	AA	TT	CT	_	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
2._RUQ_51	_	_	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
3._ICS_40	AA	TT	CT	GG	_	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
4._SPEC_160_/9	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
5._SPEC_160_/9	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
6._SPEC_160_/9	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
7._SPEC_160_/9	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
8._SPEC_160_/9	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
9._GC-08-267-8-39	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
10._GC-08-267-8-39	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
11._GC-08-267-8-39	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
12._GC-08-267-8-39	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
13._GC-08-267-8-39	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
14._UF_668	AA	TT	CT	CG	_	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
15._UF_12	AA	TT	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
16._UF_668	AA	TT	CT	CG	GG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
17._ICS_60	AA	TT	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
18._UF_676	AA	TT	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
19._ICS_39	AA	TT	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
20._ICS_40	AA	TT	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
21._ICS_60	AA	TT	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
22._UF_12	AA	TT	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
23._ICS_60	AA	TT	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X
24._RUQ_54	_	_	CT	GG	AG	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X	X_X

Input profile: SPEC_160_/9

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

Location: La Montaña, Lot 8, Row 24 4_6

Dapeng Zhang, 2016

1._SPEC_160_/9 RUQ_51

96.9 %
32 shared markers

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

Dapeng Zhang, 2016

2._SPEC_160_/9 RUQ_51

95 %
20 shared markers

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

Dapeng Zhang, 2014

3._ICS_40

94.4 %
27 shared markers

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

Location: San Juan Block2

Dapeng Zhang, 2016

4._SPEC_160_/9

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8839 1

Dapeng Zhang, 2016

Population Assignment:

Dapeng Zhang, 2016

5._SPEC_160_/9

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8839 2

Dapeng Zhang, 2016

6._SPEC_160_/9

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8839 3

Dapeng Zhang, 2016

7._SPEC_160_/9

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8839 4

Dapeng Zhang, 2016

8._SPEC_160_/9

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 8839 5

Dapeng Zhang, 2016

9._SPEC_160_/9 GC-08-267-8-39

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 1

Notes: 1

10._SPEC_160_/9 GC-08-267-8-39

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 2

Notes: 2

11._SPEC_160_/9 GC-08-267-8-39

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 3

Notes: 3

12._SPEC_160_/9 GC-08-267-8-39

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 4

Notes: 4

13._SPEC_160_/9 GC-08-267-8-39

93.9 %
33 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 5

Notes: 5

14._UF_668

92.9 %
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

15._UF_12

90.9 %
33 shared markers

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

Location: Cabiria

Dapeng Zhang, 2016

16._UF_668

90.9 %
33 shared markers

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

Dapeng Zhang, 2016

17._ICS_60

90.9 %
33 shared markers

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Indonesian Coffee and Cocoa Research Institute (ICCRI), Indonesia

Location: KW 74 I-049

Dapeng Zhang, 2016

18._UF_676

90.9 %
33 shared markers

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Indonesian Coffee and Cocoa Research Institute (ICCRI), Indonesia

Location: KW 293 I-043

Dapeng Zhang, 2016

19._ICS_39

90.9 %
33 shared markers

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Malaysian Cocoa Board (MCB), Malaysia

Location: Row 9 C0200 2A

Dapeng Zhang, 2016

20._ICS_40

90.9 %
33 shared markers

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Malaysian Cocoa Board (MCB), Malaysia

Location: C0201 2A

Dapeng Zhang, 2016

21._ICS_60

90.9 %
33 shared markers

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Malaysian Cocoa Board (MCB), Malaysia

Location: Row 8 C0202 2A

Dapeng Zhang, 2016

22._UF_12

90.9 %
33 shared markers

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

Location: 6B F444 T5

Dapeng Zhang, 2016

23._ICS_60

90.6 %
32 shared markers

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

Location: San Juan Block3

Dapeng Zhang, 2016

24._UF_221 RUQ_54

90 %
20 shared markers

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

Dapeng Zhang, 2014

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	TcSNP529	13	TcSNP534	14	TcSNP577	15	TcSNP591
16	TcSNP619	17	TcSNP645	18	TcSNP723	19	TcSNP872	20	TcSNP891
21	TcSNP917	22	TcSNP929	23	TcSNP994	24	TcSNP1062	25	TcSNP1075
26	TcSNP1165	27	TcSNP1253	28	TcSNP1270	29	TcSNP1350	30	TcSNP1414
31	TcSNP1442	32	TcSNP1458	33	TcSNP1484