SNP Profiles of SCA 6   View Data

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 Key

 1 2 3 4 5 6 7 8 9 10 11 12 13 14
_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-01-26-2-03
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-01-026-2-03
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._RUQ_234
____AC__________AA__AA______
41._SCA_6
____ACGGTT__CCCCAATT____AA__
42._GC-01-026-2-03
TTCCACGGTTGGCCCCAACTGGGGAAGG
43._SCA_6
____ACGGTT__CCCCAATT____AA__
44._SCA6
____CC__TTGGCCGGAA____GGAAGG
45._RUQ_234
AACCACCCAAGGCCGGAAAGAAGGAACC
46._MITC-000343
AACCACCCAAGGCCGGAAAGAAGGAACC
47._MITC-000344
AACCACCCAAGGCCGGAAAGAAGGAACC
48._MITC-000345
AACCACCCAAGGCCGGAAAGAAGGAACC
49._MITC-000347
AACCACCCAAGGCCGGAAAGAAGGAACC
50._MITC-000348
AACCACCCAAGGCCGGAAAGAAGGAACC
51._MITC-000349
AACCACCCAAGGCCGGAAAGAAGGAACC
52._MITC-000376
AACCACCCAAGGCCGGAAAGAAGGAACC
53._MITC-000452
AACCACCCAAGGCCGGAAAGAAGGAACC
54._SCA_6_TC_(Penn_State)_Fld#_197_Plt#_6
AACCAAACAGGGACGGAAGGAGGGAACG
55._SCA_6_Fld#_16_Plt#_1
AACCAAACAGGGACGGAAGGAGGGAACG
 15 16 17 18 19 20 21 22 23 24 25 26 27 28
_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-01-26-2-03
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-01-026-2-03
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._RUQ_234
__AA____CGCCCC__CTGGAA__CCCC
41._SCA_6
GGAACCGGCGCC__TT__GG______CC
42._GC-01-026-2-03
GGAACCGGCGCCCCTTTTGGAATTCCCC
43._SCA_6
GGAACCGGCGCC__TT__GG______CC
44._SCA6
________CGCCCC____________GG
45._RUQ_234
__AA__CCCGCCGGAA__CCAAAACCGG
46._MITC-000343
__AA__CCCGCCGGAA__CCAAAACCGG
47._MITC-000344
__AA__CCCGCCGGAA__CCAAAACCGG
48._MITC-000345
__AA__CCCGCCGGAA__CCAAAACCGG
49._MITC-000347
__AA__CCCGCCGGAA__CCAAAACCGG
50._MITC-000348
__AA__CCCGCCGGAA__CCAAAACCGG
51._MITC-000349
__AA__CCCGCCGGAA__CCAAAACCGG
52._MITC-000376
__AA__CCCGCCGGAA__CCAAAACCGG
53._MITC-000452
__AA__CCCGCCGGAA__CCAAAACCGG
54._SCA_6_TC_(Penn_State)_Fld#_197_Plt#_6
__AC__ACCGACAGAA__CCAGAAACCG
55._SCA_6_Fld#_16_Plt#_1
__AC__ACCGACAGAA__CCAGAAACCG
 29 30 31 32 33 34 35 36 37 38 39 40 41 42
_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-01-26-2-03
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-01-026-2-03
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._RUQ_234
____AACC________GG______CC__
41._SCA_6
__TTAA__CT______GG____CTCCAG
42._GC-01-026-2-03
CGTTAACCCTGGGGTTGG__CCCTCCAG
43._SCA_6
__TTAA__CC______GG____TTCCAG
44._SCA6
CGTT____CT__GGTT____CC__GG__
45._RUQ_234
__AAAA__AGCCGG__CCGGGGAGGGAG
46._MITC-000343
__AAAA__AGCCGG__CCGGGGAGGGAG
47._MITC-000344
__AAAA__AGCCGG__CCGGGGAGGGAG
48._MITC-000345
__AAAA__AGCCGG__CCGGGGAGGGAG
49._MITC-000347
__AAAA__AGCCGG__CCGGGGAGGGAG
50._MITC-000348
__AAAA__AGCCGG__CCGGGGAGGGAG
51._MITC-000349
__AAAA__AGCCGG__CCGGGGAGGGAG
52._MITC-000376
__AAAA__AGCCGG__CCGGGGAGGGAG
53._MITC-000452
__AAAA__AGCCGG__CCGGGGAGGGAG
54._SCA_6_TC_(Penn_State)_Fld#_197_Plt#_6
__AGAG__GGCCAG__ACAGAGGGCGAG
55._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 7 > FP
 Dapeng Zhang, 2016

4._SCA_6

97.9 %
24 shared markers

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

5._SCA_6

97.9 %
24 shared markers

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

6._SCA_6

97.9 %
24 shared markers

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

7._SCA_6

97.9 %
24 shared markers

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

8._SCA_6

97.9 %
24 shared markers

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

9._SCA_6

97.9 %
24 shared markers

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

10._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 10
 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 1
 Dapeng Zhang, 2016

17._SCA_6

97.9 %
24 shared markers

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Mars Center for Cocoa Science, Brazil
Location: 1203 2
 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-01-26-2-03

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

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: 15
Notes: 15
 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: 14
Notes: 14
 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: 13
Notes: 13
 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: 10
Notes: 10
 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: 9
Notes: 9
 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-01-026-2-03

97.6 %
41 shared markers

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

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 RUQ_234

96.9 %
16 shared markers

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International Cocoa Quarantine Centre, Reading (ICQC,R), United Kingdom
 Lambert Motilal, 2023
Population Assignment: 
View Data
Sca
0.997

41._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

42._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

43._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

44._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

45._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

46._SCA_6 MITC-000343

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

47._SCA_6 MITC-000344

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

48._SCA_6 MITC-000345

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

49._SCA_6 MITC-000347

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

50._SCA_6 MITC-000348

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

51._SCA_6 MITC-000349

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

52._SCA_6 MITC-000376

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

53._SCA_6 MITC-000452

43.1 %
36 shared markers

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USDA-SHRS, United States of America
 Mars, 2018

54._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

55._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