SNP Profiles of MAN-15/2 View Data

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	1	2	3	4	5	6	7	8	9	10	11	12	13	14
_Input profile	AA	CC	CC	AC	GG	AG	CC	CC	CT	CT	GG	TT	CT	CT
1._GC-05-072-2-23	AA	CC	CC	AC	GG	AG	CC	CC	CT	CT	GG	TT	CT	CT
2._GC-05-072-2-23	AA	_	CC	AC	GG	AG	CC	CC	CT	CT	GG	TT	CT	CT
3._GC-05-072-2-23	AA	_	CC	AC	GG	AG	CC	CC	CT	CT	GG	TT	CT	CT
4._GC-05-072-2-23	AA	_	CC	AC	GG	AG	CC	CC	CT	CT	GG	TT	CT	CT
5._MAN_15_/2_[BRA]	AA	CC	CC	AC	_	_	_	_	CT	CT	GG	_	CT	_
6._MAN_15_/2_[BRA]	AA	CC	CC	AC	_	_	_	_	CT	CT	GG	_	CT	_
7._MAN_15_/2_[BRA]	AA	_	CC	AC	_	_	_	_	CT	CT	GG	_	CT	_
8._MAN_15_/2_[BRA]	AA	_	CC	AC	_	_	_	_	CT	CT	GG	_	CT	_
9._MAN_15_/2_[BRA]	AA	_	CC	AC	_	_	_	_	CT	CT	GG	_	CT	_
10._RUQ_86	_	_	CC	AC	_	_	CC	_	CT	_	_	TT	TT	_
11._MAN_15_/2_[BRA]	AA	CC	CC	AC	_	_	_	_	CT	CT	GG	_	CT	_
12._MAN_15_/2_[BRA]	AA	CC	CC	AC	_	_	_	_	CT	CT	GG	_	CT	_
13._RUQ_86	AA	CC	CC	AC	_	_	_	_	CT	CT	GG	_	CT	_
14._RUQ_86	_	_	_	AC	_	_	CC	_	_	_	_	_	_	_
15._MAN15/2[BRA]	_	_	_	AC	_	_	_	_	CT	_	_	_	CT	_
16._MAN_15_/2_[BRA]	_	AA	CT	AA	_	_	_	_	CC	CC	GG	_	CC	_
17._RUQ_86	AA	CC	_	AC	GG	GG	_	GG	AG	_	GG	AA	AG	AG

	15	16	17	18	19	20	21	22	23	24	25	26	27	28
_Input profile	AT	CC	AA	GG	GG	CC	GG	CT	AA	TT	GG	AT	AA	CG
1._GC-05-072-2-23	AT	CC	AA	GG	GG	CC	GG	CT	AA	TT	GG	AT	AA	CG
2._GC-05-072-2-23	AT	CC	AA	GG	GG	CC	GG	CT	AA	TT	GG	AT	AA	CG
3._GC-05-072-2-23	AT	CC	AA	GG	GG	CC	GG	CT	AA	TT	GG	AT	AA	CG
4._GC-05-072-2-23	AT	CC	AA	GG	GG	CC	GG	CT	AA	TT	GG	AT	AA	CG
5._MAN_15_/2_[BRA]	_	_	_	GG	_	_	GG	_	_	_	_	AT	AA	_
6._MAN_15_/2_[BRA]	_	_	_	GG	_	_	GG	_	_	_	_	AT	AA	_
7._MAN_15_/2_[BRA]	_	_	_	GG	_	_	GG	_	_	_	_	AT	AA	_
8._MAN_15_/2_[BRA]	_	_	_	GG	_	_	GG	_	_	_	_	AT	AA	_
9._MAN_15_/2_[BRA]	_	_	_	GG	_	_	GG	_	_	_	_	AT	AA	_
10._RUQ_86	_	_	_	_	_	CC	_	_	_	_	GG	_	AA	-
11._MAN_15_/2_[BRA]	_	_	_	AG	_	_	GG	_	_	_	_	AT	AA	_
12._MAN_15_/2_[BRA]	_	_	_	AG	_	_	GG	_	_	_	_	AT	AA	_
13._RUQ_86	_	_	_	AG	_	_	GG	_	_	_	_	AT	AA	_
14._RUQ_86	_	_	_	AG	TT	_	_	_	_	_	_	_	_	_
15._MAN15/2[BRA]	_	_	AG	_	_	GG	_	CT	_	_	GG	_	AA	CC
16._MAN_15_/2_[BRA]	_	_	_	AA	_	_	GG	_	_	_	_	TT	AA	_
17._RUQ_86	AT	AC	AG	AG	CC	_	GG	AG	AA	AA	GG	AT	AA	CG

	29	30	31	32	33	34	35	36	37	38	39	40	41	42
_Input profile	GG	AA	TT	GG	AG	CG	CC	AA	GT	GG	GT	AA	CT	GG
1._GC-05-072-2-23	GG	AA	TT	GG	AG	CG	CC	AA	GT	GG	GT	AA	CT	GG
2._GC-05-072-2-23	GG	AA	TT	GG	AG	CG	CC	AA	GT	GG	GT	AA	CT	GG
3._GC-05-072-2-23	GG	AA	TT	GG	AG	CG	CC	AA	GT	GG	GT	AA	CT	GG
4._GC-05-072-2-23	GG	AA	TT	GG	AG	CG	CC	AA	GT	GG	GT	AA	CT	GG
5._MAN_15_/2_[BRA]	GG	AA	_	_	_	CG	_	AA	GT	_	_	AA	_	_
6._MAN_15_/2_[BRA]	GG	AA	_	_	_	CG	_	AA	GT	_	_	AA	_	_
7._MAN_15_/2_[BRA]	GG	AA	_	_	_	CG	_	AA	GT	_	_	AA	_	_
8._MAN_15_/2_[BRA]	GG	AA	_	_	_	CG	_	AA	GT	_	_	AA	_	_
9._MAN_15_/2_[BRA]	GG	AA	_	_	_	CG	_	AA	GT	_	_	AA	_	_
10._RUQ_86	GG	_	_	_	AG	CG	CC	AA	GT	_	_	AA	CT	_
11._MAN_15_/2_[BRA]	GG	AA	_	_	_	GG	_	AA	GT	_	_	AA	_	_
12._MAN_15_/2_[BRA]	GG	AA	_	_	_	GG	_	AA	GT	_	_	AA	_	_
13._RUQ_86	GG	AA	_	_	_	GG	_	AA	GT	_	_	AG	_	_
14._RUQ_86	GG	_	_	_	_	GG	_	AA	_	_	_	_	CT	_
15._MAN15/2[BRA]	CC	_	_	_	AG	CG	_	_	_	_	GT	_	CT	_
16._MAN_15_/2_[BRA]	GG	AA	_	_	_	CG	_	AA	GG	_	_	AA	_	_
17._RUQ_86	CC	AA	AA	CC	AG	CG	CC	AA	AC	CC	AC	AA	AG	AG

	43	44	45	46	47	48	49	50	51	52	53	54	55	56
_Input profile	CC	GG	TT	TT	AA	AG	AA	CC	AC	GG	AG	GT	TT	CC
1._GC-05-072-2-23	CC	GG	TT	TT	AA	AG	AA	CC	AC	GG	AG	GT	TT	CC
2._GC-05-072-2-23	CC	GG	TT	TT	AA	AG	AA	CC	AC	GG	AG	GT	TT	CC
3._GC-05-072-2-23	CC	GG	TT	TT	AA	AG	AA	CC	AC	GG	AG	GT	TT	CC
4._GC-05-072-2-23	CC	GG	TT	TT	AA	AG	AA	CC	AC	GG	AG	GT	TT	CC
5._MAN_15_/2_[BRA]	_	_	_	TT	_	_	_	_	_	_	_	_	_	CC
6._MAN_15_/2_[BRA]	_	_	_	TT	_	_	_	_	_	_	_	_	_	CC
7._MAN_15_/2_[BRA]	_	_	_	TT	_	_	_	_	_	_	_	_	_	CC
8._MAN_15_/2_[BRA]	_	_	_	TT	_	_	_	_	_	_	_	_	_	CC
9._MAN_15_/2_[BRA]	_	_	_	TT	_	_	_	_	_	_	_	_	_	CC
10._RUQ_86	_	GG	TT	_	_	AG	_	_	_	_	_	_	CT	CT
11._MAN_15_/2_[BRA]	_	_	_	TT	_	_	_	_	_	_	_	_	_	CT
12._MAN_15_/2_[BRA]	_	_	_	TT	_	_	_	_	_	_	_	_	_	CT
13._RUQ_86	_	_	_	TT	_	_	_	_	_	_	_	_	_	CT
14._RUQ_86	_	_	_	_	_	AG	_	_	_	_	_	_	_	_
15._MAN15/2[BRA]	_	_	TT	_	AA	_	_	_	_	_	_	_	_	CT
16._MAN_15_/2_[BRA]	_	_	_	TT	_	_	_	_	_	_	_	_	_	CT
17._RUQ_86	GG	CC	_	AA	_	AG	AA	GG	_	GG	AA	AC	AG	AG

	57	58	59	60	61	62	63	64	65	66	67	68	69	70
_Input profile	CC	TT	GG	CG	CT	CC	AA	GG	GG	CC	AA	GT	GG	AG
1._GC-05-072-2-23	CC	TT	GG	CG	CT	CC	AA	GG	GG	CC	AA	GT	GG	AG
2._GC-05-072-2-23	CC	TT	GG	CG	CT	CC	AA	GG	GG	CC	AA	GT	GG	AG
3._GC-05-072-2-23	CC	TT	GG	CG	CT	CC	AA	GG	GG	CC	AA	GT	GG	AG
4._GC-05-072-2-23	CC	TT	GG	CG	CT	CC	AA	GG	GG	CC	AA	GT	GG	AG
5._MAN_15_/2_[BRA]	CC	_	_	CG	_	CC	AA	GG	_	CC	AA	GT	GG	_
6._MAN_15_/2_[BRA]	CC	_	_	CG	_	CC	AA	GG	_	CC	AA	GT	GG	_
7._MAN_15_/2_[BRA]	CC	_	_	CG	_	CC	AA	GG	_	CC	AA	GT	GG	_
8._MAN_15_/2_[BRA]	CC	_	_	CG	_	CC	AA	GG	_	CC	AA	GT	GG	_
9._MAN_15_/2_[BRA]	CC	_	_	CG	_	CC	AA	GG	_	CC	AA	GT	GG	_
10._RUQ_86	_	TT	-	CG	CT	CC	AC	_	GG	CC	AG	GT	GG	AG
11._MAN_15_/2_[BRA]	CC	_	_	CG	_	CC	AC	GG	_	CC	AG	GT	GG	_
12._MAN_15_/2_[BRA]	CC	_	_	CG	_	CC	AC	GG	_	CC	AG	GT	GG	_
13._RUQ_86	CC	_	_	CG	_	CC	AC	GG	_	CC	AG	GT	GG	_
14._RUQ_86	_	_	AG	_	_	_	_	_	_	CC	AG	_	GG	AG
15._MAN15/2[BRA]	_	_	_	CG	CT	_	AC	_	GG	CC	AG	_	_	_
16._MAN_15_/2_[BRA]	_	_	_	CG	_	CC	AC	GG	_	CC	GG	TT	GG	_
17._RUQ_86	GG	AA	AG	CG	AG	GG	AC	GG	GG	CC	AG	AC	CC	AG

	71	72	73	74	75	76	77	78	79	80	81	82	83	84
_Input profile	CC	CG	AA	CT	CC	AG	AC	AC	AG	AC	CG	CC	AA	AC
1._GC-05-072-2-23	CC	CG	AA	CT	CC	AG	AC	AC	AG	AC	CG	CC	AA	AC
2._GC-05-072-2-23	CC	CG	AA	CT	CC	AG	AC	AC	AG	AC	CG	CC	AA	AC
3._GC-05-072-2-23	CC	CG	AA	CT	CC	AG	AC	AC	AG	AC	CG	CC	AA	AC
4._GC-05-072-2-23	CC	CG	AA	CT	CC	AG	AC	AC	AG	AC	CG	CC	AA	AC
5._MAN_15_/2_[BRA]	_	_	AA	CT	_	_	_	_	_	AC	CG	_	_	_
6._MAN_15_/2_[BRA]	_	_	AA	CT	_	_	_	_	_	AC	CG	_	_	_
7._MAN_15_/2_[BRA]	_	_	AA	CT	_	_	_	_	_	AC	CG	_	_	_
8._MAN_15_/2_[BRA]	_	_	AA	CT	_	_	_	_	_	AC	CG	_	_	_
9._MAN_15_/2_[BRA]	_	_	AA	CT	_	_	_	_	_	AC	CG	_	_	_
10._RUQ_86	_	_	_	_	_	_	_	_	_	AC	CG	_	_	AC
11._MAN_15_/2_[BRA]	_	_	AA	CT	_	_	_	_	_	AC	CG	_	_	_
12._MAN_15_/2_[BRA]	_	_	AA	CT	_	_	_	_	_	AC	CG	_	_	_
13._RUQ_86	_	_	AA	CT	_	_	_	_	_	AC	CG	_	_	_
14._RUQ_86	_	_	AA	_	_	_	_	_	_	AC	CG	_	_	AC
15._MAN15/2[BRA]	_	CG	_	_	_	_	_	_	_	_	CG	_	_	_
16._MAN_15_/2_[BRA]	_	_	AA	TT	_	_	_	_	_	CC	GG	_	_	_
17._RUQ_86	_	_	_	AG	CC	AG	AC	AC	_	AC	CG	GG	AA	AC

	85	86	87	88	89	90	91	92	93	94	95
_Input profile	CC	CT	TT	TT	AG	CC	TT	GT	CT	AT	GG	X_X	X_X	X_X
1._GC-05-072-2-23	CC	CT	TT	TT	AG	CC	TT	GT	CT	AT	GG	X_X	X_X	X_X
2._GC-05-072-2-23	CC	CT	TT	TT	AG	CC	TT	GT	CT	AT	GG	X_X	X_X	X_X
3._GC-05-072-2-23	CC	CT	TT	TT	AG	CC	TT	GT	CT	AT	GG	X_X	X_X	X_X
4._GC-05-072-2-23	CC	CT	TT	TT	AG	CC	TT	GT	CT	AT	GG	X_X	X_X	X_X
5._MAN_15_/2_[BRA]	CC	CT	TT	_	AG	_	TT	GT	CT	_	_	X_X	X_X	X_X
6._MAN_15_/2_[BRA]	CC	CT	TT	_	AG	_	TT	GT	CT	_	_	X_X	X_X	X_X
7._MAN_15_/2_[BRA]	CC	CT	TT	_	AG	_	TT	GT	CT	_	_	X_X	X_X	X_X
8._MAN_15_/2_[BRA]	CC	CT	TT	_	AG	_	TT	GT	CT	_	_	X_X	X_X	X_X
9._MAN_15_/2_[BRA]	CC	CT	TT	_	AG	_	TT	GT	CT	_	_	X_X	X_X	X_X
10._RUQ_86	CC	_	_	_	AG	CC	TT	-	_	_	_	X_X	X_X	X_X
11._MAN_15_/2_[BRA]	CC	CT	TT	_	AG	_	TT	GT	CT	_	_	X_X	X_X	X_X
12._MAN_15_/2_[BRA]	CC	_	TT	_	AG	_	TT	GT	CT	_	_	X_X	X_X	X_X
13._RUQ_86	CC	CT	TT	_	AG	_	TT	GT	CT	_	_	X_X	X_X	X_X
14._RUQ_86	_	_	TT	_	_	CC	_	GT	_	_	_	X_X	X_X	X_X
15._MAN15/2[BRA]	_	CT	_	_	_	_	_	_	_	_	_	X_X	X_X	X_X
16._MAN_15_/2_[BRA]	CT	TT	_	_	AA	_	CC	TT	_	_	_	X_X	X_X	X_X
17._RUQ_86	GG	AG	_	AA	_	_	AA	AA	AG	AT	GG	X_X	X_X	X_X

Input profile: MAN_15_/2_[BRA] GC-05-072-2-23

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Mars Center for Cocoa Science, Brazil

Location: Tree: 2

Notes: 2 > FP2

1._MAN_15_/2_[BRA] GC-05-072-2-23

identical
95 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 5

Notes: 5 > FP4

2._MAN_15_/2_[BRA] GC-05-072-2-23

identical
94 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 4

Notes: 4

3._MAN_15_/2_[BRA] GC-05-072-2-23

identical
94 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 3

Notes: 3 > FP3

4._MAN_15_/2_[BRA] GC-05-072-2-23

identical
94 shared markers

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Mars Center for Cocoa Science, Brazil

Location: Tree: 1

Notes: 1 > FP1

5._MAN_15_/2_[BRA]

identical
40 shared markers

View View all Clone Any

Mars Center for Cocoa Science, Brazil

Location: 5223 5 > FP

Dapeng Zhang, 2016

6._MAN_15_/2_[BRA]

identical
40 shared markers

View View all Clone Any

Mars Center for Cocoa Science, Brazil

Location: 5223 2 > FP

Dapeng Zhang, 2016

7._MAN_15_/2_[BRA]

identical
39 shared markers

View View all Clone Any

Mars Center for Cocoa Science, Brazil

Location: 5223 3 > FP

Dapeng Zhang, 2016

8._MAN_15_/2_[BRA]

identical
39 shared markers

View View all Clone Any

Mars Center for Cocoa Science, Brazil

Location: 5223 1 > FP

Dapeng Zhang, 2016

9._MAN_15_/2_[BRA]

identical
39 shared markers

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Mars Center for Cocoa Science, Brazil

Location: 5223 4

Dapeng Zhang, 2016

Population Assignment:

Dapeng Zhang, 2016

10._MAN_15_/2_[BRA] RUQ_86

93.8 %
40 shared markers

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

Dapeng Zhang, 2014

11._MAN_15_/2_[BRA]

93.8 %
40 shared markers

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Malaysian Cocoa Board (MCB), Malaysia

Location: C0297

Dapeng Zhang, 2016

12._MAN_15_/2_[BRA]

93.6 %
39 shared markers

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

Location: 5A N3/476 T2

Dapeng Zhang, 2016

13._MAN_15_/2_[BRA] RUQ_86

92.5 %
40 shared markers

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

Dapeng Zhang, 2016

14._MAN_15_/2_[BRA] RUQ_86

85.7 %
21 shared markers

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

Lambert Motilal, 2023

15._MAN_15_/2_[BRA] MAN15/2[BRA]

82.7 %
26 shared markers

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Center for Forestry Research and Technology Transfer, Vietnam

Location: CEFORTT

Jocelyn De Wever et al., 2019

16._MAN_15_/2_[BRA]

65.3 %
36 shared markers

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

Location: La Montaña Lot 6 Row 53 46-48

Dapeng Zhang, 2016

17._MAN_15_/2_[BRA] RUQ_86

50 %
81 shared markers

View View all Clone Any

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

Notes: Reading_Collection

Key to SNP Markers

Key to SNP Markers

1	TcSNP1075	2	TcSNP1350	3	TcSNP534	4	TcSNP591	5	TcSNP42
6	TcSNP418	7	TcSNP702	8	TcSNP1096	9	TcSNP1060	10	TcSNP1165
11	TcSNP429	12	TcSNP75	13	TcSNP891	14	TcSNP122	15	TcSNP316
16	TcSNP521	17	TcSNP860	18	TcSNP1062	19	TcSNP836	20	TcSNP878
21	TcSNP929	22	TcSNP413	23	TcSNP653	24	TcSNP1149	25	TcSNP174
26	TcSNP32	27	TcSNP372	28	TcSNP448	29	TcSNP872	30	TcSNP953
31	TcSNP1034	32	TcSNP1175	33	TcSNP1111	34	TcSNP577	35	TcSNP90
36	TcSNP998	37	TcSNP150	38	TcSNP28	39	TcSNP751	40	TcSNP1484
41	TcSNP602	42	TcSNP561	43	TcSNP894	44	TcSNP1063	45	TcSNP1126
46	TcSNP1270	47	TcSNP606	48	TcSNP329	49	TcSNP689	50	TcSNP944
51	TcSNP1242	52	TcSNP1383	53	TcSNP547	54	TcSNP776	55	TcSNP1309
56	TcSNP151	57	TcSNP1520	58	TcSNP799	59	TcSNP899	60	TcSNP226
61	TcSNP1439	62	TcSNP1442	63	TcSNP193	64	TcSNP25	65	TcSNP364
66	TcSNP144	67	TcSNP230	68	TcSNP560	69	TcSNP723	70	TcSNP731
71	TcSNP701	72	TcSNP1041	73	TcSNP645	74	TcSNP917	75	Tcm003s01336581
76	Tcm003s07402719	77	Tcm001s00947643	78	Tcm006s26664133	79	Tcm002s20575712	80	TcSNP529
81	TcSNP1458	82	TcSNP60	83	TcSNP430	84	TcSNP823	85	TcSNP619
86	TcSNP994	87	TcSNP1144	88	TcSNP1156	89	TcSNP469	90	TcSNP999
91	TcSNP242	92	TcSNP1253	93	TcSNP1414	94	TcSNP154	95	TcSNP240