SNP Profiles of SCA 6   View Data

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 Key

 1234567891011121314
_Input profile
TTCCCCGGTTGGCCCCAACTAAGGAAGG
1._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
2._SCA_6
__ACGGTT_CCCCAACT__AA_
3._SCA_6
__ACGGTT_CCCCAACT__AA_
4._SCA_6
__ACGGTT_CCCCAACT__AA_
5._SCA_6
__ACGGTT_CCCCAACT__AA_
6._SCA_6
__ACGGTT_CCCCAACT__AA_
7._SCA_6
__ACGGTT_CCCCAACT__AA_
8._SCA_6
__ACGGTT_CCCCAACT__AA_
9._SCA_6
__ACGGTT_CCCCAACT__AA_
10._SCA_6
__ACGGTT_CCCCAACT__AA_
11._SCA_6
__ACGGTT_CCCCAACT__AA_
12._SCA_6
__ACGGTT_CCCCAACT__AA_
13._SCA_6
__ACGGTT_CCCCAACT__AA_
14._SCA_6
__ACGGTT_CCCCAACT__AA_
15._SCA_6
__ACGGTT_CCCCAACT__AA_
16._SCA_6
__ACGGTT_CCCCAACT__AA_
17._SCA_6
__ACGGTT_CCCCAACT__AA_
18._SCA_6
__ACGGTT_CCCCAACT__AA_
19._RUQ_234
__ACGGTT_CCCCAACT__AA_
20._SCA_6
__ACGGTT_CCCCAACT__AA_
21._SCA_6
__ACGGTT_CCCCAACT__AA_
22._SCA_6
__ACGGTT_CCCCAACT__AA_
23._SCA_6
__ACGGTT_CCCCAACT__AA_
24._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
25._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
26._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
27._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
28._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
29._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
30._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
31._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
32._GC-01-26-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
33._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
34._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
35._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
36._GC-01-26-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
37._GC-01-26-2-03
TTCCACGGTTGGCCCCAACTAAGGAAGG
38._GC-01-26-2-03
TTCCACGGTTGGCCCCAACT_GGAAGG
39._RUQ_234B
__AC_____AA_AA___
40._SCA_6
__ACGGTT_CCCCAATT__AA_
41._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTGGGGAAGG
42._SCA_6
__ACGGTT_CCCCAATT__AA_
43._SCA6
__CC_TTGGCCGGAA__GGAAGG
44._RUQ_234
AACCACCCAAGGCCGGAAAGAAGGAACC
45._MITC-000343
AACCACCCAAGGCCGGAAAGAAGGAACC
46._MITC-000344
AACCACCCAAGGCCGGAAAGAAGGAACC
47._MITC-000345
AACCACCCAAGGCCGGAAAGAAGGAACC
48._MITC-000347
AACCACCCAAGGCCGGAAAGAAGGAACC
49._MITC-000348
AACCACCCAAGGCCGGAAAGAAGGAACC
50._MITC-000349
AACCACCCAAGGCCGGAAAGAAGGAACC
51._MITC-000376
AACCACCCAAGGCCGGAAAGAAGGAACC
52._MITC-000452
AACCACCCAAGGCCGGAAAGAAGGAACC
53._SCA_6_TC_(Penn_State)_Fld#_197_Plt#_6
AACCAAACAGGGACGGAAGGAGGGAACG
54._SCA_6_Fld#_16_Plt#_1
AACCAAACAGGGACGGAAGGAGGGAACG
 1516171819202122232425262728
_Input profile
GGAACCGGCGCCCCTTCTGGAATTCCCC
1._GC-01-026-2-03
GGAACCGGCGCCCCTT_GGAATTCCCC
2._SCA_6
GGAACCGGCGCC_TT_GG___CC
3._SCA_6
GGAACCGGCGCC_TT_GG___CC
4._SCA_6
GGAACCGGCGCC_TT_GG___CC
5._SCA_6
GGAACCGGCGCC_TT_GG___CC
6._SCA_6
GGAACCGGCGCC_TT_GG___CC
7._SCA_6
GGAACCGGCGCC_TT_GG___CC
8._SCA_6
GGAACCGGCGCC_TT_GG___CC
9._SCA_6
GGAACCGGCGCC_TT_GG___CC
10._SCA_6
GGAACCGGCGCC_TT_GG___CC
11._SCA_6
GGAACCGGCGCC_TT_GG___CC
12._SCA_6
GGAACCGGCGCC_TT_GG___CC
13._SCA_6
GGAACCGGCGCC_TT_GG___CC
14._SCA_6
GGAACCGGCGCC_TT_GG___CC
15._SCA_6
GGAACCGGCGCC_TT_GG___CC
16._SCA_6
GGAACCGGCGCC_TT_GG___CC
17._SCA_6
GGAACCGGCGCC_TT_GG___CC
18._SCA_6
GGAACCGGCGCC_TT_GG___CC
19._RUQ_234
GGAACCGGCGCC_TT_GG___CC
20._SCA_6
GGAACCGGCGCC_TT_GG___CC
21._SCA_6
GGAACCGGCGCC_TT_GG___CC
22._SCA_6
GGAACCGGCGCC_TT_GG___CC
23._SCA_6
GGAACCGGCGCC_TT_GG___CC
24._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
25._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
26._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
27._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
28._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
29._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
30._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
31._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
32._GC-01-26-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
33._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
34._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
35._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
36._GC-01-26-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
37._GC-01-26-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
38._GC-01-26-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
39._RUQ_234B
_AA__CGCCCC_CTGGAA_CCCC
40._SCA_6
GGAACCGGCGCC_TT_GG___CC
41._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
42._SCA_6
GGAACCGGCGCC_TT_GG___CC
43._SCA6
____CGCCCC______GG
44._RUQ_234
_AA_CCCGCCGGAA_CCAAAACCGG
45._MITC-000343
_AA_CCCGCCGGAA_CCAAAACCGG
46._MITC-000344
_AA_CCCGCCGGAA_CCAAAACCGG
47._MITC-000345
_AA_CCCGCCGGAA_CCAAAACCGG
48._MITC-000347
_AA_CCCGCCGGAA_CCAAAACCGG
49._MITC-000348
_AA_CCCGCCGGAA_CCAAAACCGG
50._MITC-000349
_AA_CCCGCCGGAA_CCAAAACCGG
51._MITC-000376
_AA_CCCGCCGGAA_CCAAAACCGG
52._MITC-000452
_AA_CCCGCCGGAA_CCAAAACCGG
53._SCA_6_TC_(Penn_State)_Fld#_197_Plt#_6
_AC_ACCGACAGAA_CCAGAAACCG
54._SCA_6_Fld#_16_Plt#_1
_AC_ACCGACAGAA_CCAGAAACCG
 2930313233343536373839404142
_Input profile
CGTTAACCCTGGGGTTGGCCCCCTCCAG
1._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
2._SCA_6
_TTAA_CT___GG__CTCCAG
3._SCA_6
_TTAA_CT___GG__CTCCAG
4._SCA_6
_TTAA_CT___GG__CTCCAG
5._SCA_6
_TTAA_CT___GG__CTCCAG
6._SCA_6
_TTAA_CT___GG__CTCCAG
7._SCA_6
_TTAA_CT___GG__CTCCAG
8._SCA_6
_TTAA_CT___GG__CTCCAG
9._SCA_6
_TTAA_CT___GG__CTCCAG
10._SCA_6
_TTAA_CT___GG__CTCCAG
11._SCA_6
_TTAA_CT___GG__CTCCAG
12._SCA_6
_TTAA_CT___GG__CTCCAG
13._SCA_6
_TTAA_CT___GG__CTCCAG
14._SCA_6
_TTAA_CT___GG__CTCCAG
15._SCA_6
_TTAA_CT___GG__CTCCAG
16._SCA_6
_TTAA_CT___GG__CTCCAG
17._SCA_6
_TTAA_CT___GG__CTCCAG
18._SCA_6
_TTAA_CT___GG__CTCCAG
19._RUQ_234
_TTAA_CT___GG__CTCCAG
20._SCA_6
_TTAA_CT___GG__CTCCAG
21._SCA_6
_TTAA_CT___GG__CTCCAG
22._SCA_6
_TTAA_CT___GG__CTCCAG
23._SCA_6
_TTAA_CT___GG__CTCCAG
24._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
25._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
26._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
27._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
28._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
29._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
30._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
31._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
32._GC-01-26-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
33._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
34._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
35._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
36._GC-01-26-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
37._GC-01-26-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
38._GC-01-26-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
39._RUQ_234B
__AACC____GG___CC_
40._SCA_6
_TTAA_CT___GG__CTCCAG
41._GC-01-026-2-03
CGTTAACCCTGGGGTTGG_CCCTCCAG
42._SCA_6
_TTAA_CC___GG__TTCCAG
43._SCA6
CGTT__CT_GGTT__CC_GG_
44._RUQ_234
_AAAA_AGCCGG_CCGGGGAGGGAG
45._MITC-000343
_AAAA_AGCCGG_CCGGGGAGGGAG
46._MITC-000344
_AAAA_AGCCGG_CCGGGGAGGGAG
47._MITC-000345
_AAAA_AGCCGG_CCGGGGAGGGAG
48._MITC-000347
_AAAA_AGCCGG_CCGGGGAGGGAG
49._MITC-000348
_AAAA_AGCCGG_CCGGGGAGGGAG
50._MITC-000349
_AAAA_AGCCGG_CCGGGGAGGGAG
51._MITC-000376
_AAAA_AGCCGG_CCGGGGAGGGAG
52._MITC-000452
_AAAA_AGCCGG_CCGGGGAGGGAG
53._SCA_6_TC_(Penn_State)_Fld#_197_Plt#_6
_AGAG_GGCCAG_ACAGAGGGCGAG
54._SCA_6_Fld#_16_Plt#_1
_AGAG_GGCCAG_ACAGAGGGCGAG

Input profile: SCA_6 RUQ_234

 
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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom
 Dapeng Zhang, 2014

1._SCA_6 GC-01-026-2-03

98.8 %
40 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 2
Notes: 2
 Mars, 2018

2._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 9
 Dapeng Zhang, 2016

3._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 16 > F
 Dapeng Zhang, 2016

4._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 11 > F
 Dapeng Zhang, 2016

5._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 1 > FP
 Dapeng Zhang, 2016

6._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 15
 Dapeng Zhang, 2016

7._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 14
 Dapeng Zhang, 2016

8._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 13
 Dapeng Zhang, 2016

9._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 10
 Dapeng Zhang, 2016

10._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 7 > FP
 Dapeng Zhang, 2016

11._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 8
 Dapeng Zhang, 2016

12._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 6
 Dapeng Zhang, 2016

13._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 5
 Dapeng Zhang, 2016

14._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 4
 Dapeng Zhang, 2016

15._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 3
 Dapeng Zhang, 2016

16._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 2
 Dapeng Zhang, 2016

17._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 1
 Dapeng Zhang, 2016
Population Assignment: 
View Data
 Dapeng Zhang, 2016

18._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 2
 Dapeng Zhang, 2016

19._SCA_6 RUQ_234

97.9 %
24 shared markers

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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom
 Dapeng Zhang, 2016

20._SCA_6

97.9 %
24 shared markers

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Cocoa Research Institute of Ghana (CRIG), Ghana
Location: P75 279
 Dapeng Zhang, 2016

21._SCA_6

97.9 %
24 shared markers

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Cocoa Research Institute of Ghana (CRIG), Ghana
Location: P76 278
 Dapeng Zhang, 2016

22._SCA_6

97.9 %
24 shared markers

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Malaysian Cocoa Board (MCB), Malaysia
Location: C0267
 Dapeng Zhang, 2016

23._SCA_6

97.9 %
24 shared markers

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International Cocoa Genebank, Trinidad (ICG,T), Trinidad and Tobago
Location: Marper D 644
 Dapeng Zhang, 2016

24._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 5
Notes: 5
 Mars, 2018

25._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 14
Notes: 14
 Mars, 2018

26._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 13
Notes: 13
 Mars, 2018

27._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 10
Notes: 10
 Mars, 2018

28._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 9
Notes: 9
 Mars, 2018

29._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 15
Notes: 15
 Mars, 2018

30._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 8
Notes: 8
 Mars, 2018

31._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 6
Notes: 6
 Mars, 2018

32._SCA_6 GC-01-26-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Field: 1, Block: 2, Rep: 3, Tree: PL1
Notes: PL1 FP1
 Mars, 2018

33._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 4
Notes: 4
 Mars, 2018

34._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 2
Notes: 2
 Mars, 2018

35._SCA_6 GC-01-026-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 1
Notes: Dead
 Mars, 2018

36._SCA_6 GC-01-26-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Field: 1, Block: 2, Rep: 3, Tree: PL16
Notes: PL16 FP4
 Mars, 2018

37._SCA_6 GC-01-26-2-03

97.6 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Field: 1, Block: 2, Rep: 3, Tree: PL7
Notes: PL7 FP3
 Mars, 2018

38._SCA_6 GC-01-26-2-03

97.5 %
40 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Field: 1, Block: 2, Rep: 3, Tree: PL11
Notes: PL11 FP2
 Mars, 2018

39._SCA_6 RUQ_234B

96.9 %
16 shared markers

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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom
 Lambert Motilal, 2023

40._SCA_6

95.8 %
24 shared markers

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Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Costa Rica
Location: Cabiria
 Dapeng Zhang, 2016

41._SCA_6 GC-01-026-2-03

95.1 %
41 shared markers

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Mars Center for Cocoa Science, Brazil
Location: Tree: 3
Notes: 3
 Mars, 2018

42._SCA_6

91.7 %
24 shared markers

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Indonesian Coffee and Cocoa Research Institute (ICCRI), Indonesia
Location: KW 268 I-022
 Dapeng Zhang, 2016

43._SCA_6 SCA6

85 %
20 shared markers

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Center for Forestry Research and Technology Transfer, Vietnam
Location: CEFORTT
 Jocelyn De Wever et al., 2019

44._SCA_6 RUQ_234

43.1 %
36 shared markers

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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom
Notes: Reading_Collection
 Mars, 2018

45._SCA_6 MITC-000343

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

46._SCA_6 MITC-000344

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

47._SCA_6 MITC-000345

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

48._SCA_6 MITC-000347

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

49._SCA_6 MITC-000348

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

50._SCA_6 MITC-000349

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

51._SCA_6 MITC-000376

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

52._SCA_6 MITC-000452

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

53._SCA_6 SCA_6_TC_(Penn_State)_Fld#_197_Plt#_6

34.7 %
36 shared markers

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USDA-TARS, United States of America
Location: Field: 197, Tree: 6
Notes: TARS_Cacao_collection
 Mars, 2018

54._SCA_6 SCA_6_Fld#_16_Plt#_1

34.7 %
36 shared markers

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USDA-TARS, United States of America
Location: Field: 16, Tree: 1
 Mars, 2018

 

  Key to SNP Markers

1TcSNP75 2TcSNP90 3TcSNP144 4TcSNP150 5TcSNP151
6TcSNP174 7TcSNP193 8TcSNP226 9TcSNP230 10TcSNP242
11TcSNP329 12TcSNP364 13TcSNP372 14TcSNP448 15TcSNP469
16TcSNP529 17TcSNP534 18TcSNP560 19TcSNP577 20TcSNP591
21TcSNP602 22TcSNP619 23TcSNP702 24TcSNP723 25TcSNP731
26TcSNP799 27TcSNP823 28TcSNP872 29TcSNP878 30TcSNP891
31TcSNP998 32TcSNP999 33TcSNP1060 34TcSNP1063 35TcSNP1111
36TcSNP1126 37TcSNP1253 38TcSNP1309 39TcSNP1439 40TcSNP1442
41TcSNP1458 42TcSNP1484