| | |
Sequenom MassARRAY
|
TASSEL
|
|---|
|
SNP ID
|
Position
|
Genotype
|
MF
|
MAF
|
Genotype
|
MF
|
MAF
|
|---|
|
S14_2062712
|
2062712
|
GG/GT
|
0.72
|
0.28
|
GG/GT
|
0.72
|
0.28
|
|
S14_2846470
|
2846470
|
CC/TC
|
0.72
|
0.28
|
CC/TC
|
0.72
|
0.28
|
|
S14_3066185
|
3066185
|
AA/GA
|
0.72
|
0.28
|
AA/GA
|
0.72
|
0.28
|
|
S14_3222720
|
3222720
|
TT/TA
|
0.72
|
0.28
|
TT/TA
|
0.72
|
0.28
|
|
S14_3296164
|
3296164
|
CC/TC
|
0.72
|
0.28
|
CC/TC
|
0.72
|
0.28
|
|
S14_3596942
|
3596942
|
CC/CT
|
0.72
|
0.28
|
CC/CT
|
0.72
|
0.28
|
|
S14_4065142
|
4065142
|
TT/GT
|
0.72
|
0.28
|
TT/GT
|
0.72
|
0.28
|
|
S14_4196799
|
4196799
|
AA/AG
|
0.72
|
0.28
|
AA/AG
|
0.72
|
0.28
|
|
S14_4921219
|
4921219
|
CC/CT
|
0.74
|
0.26
|
CC/CT
|
0.74
|
0.26
|
|
S14_5274160
|
5274160
|
TT/CT
|
0.74
|
0.26
|
TT/CT
|
0.74
|
0.26
|
|
S14_5737727
|
5737727
|
AA/TA
|
0.74
|
0.26
|
AA/TA
|
0.74
|
0.26
|
|
S14_5771919
|
5771919
|
AA/CA
|
0.74
|
0.26
|
AA/CA
|
0.74
|
0.26
|
|
S14_5804788
|
5804788
|
AA/GA
|
0.74
|
0.26
|
AA/GA
|
0.74
|
0.26
|
|
S14_6008125
|
6008125
|
GG/CG
|
0.74
|
0.26
|
GG/CG
|
0.74
|
0.26
|
|
S14_6071298
|
6071298
|
GG/AG
|
0.74
|
0.26
|
GG/AG
|
0.74
|
0.26
|
|
S14_6071669
|
6071669
|
CC/CA
|
0.74
|
0.26
|
CC/CA
|
0.74
|
0.26
|
|
S14_6175917
|
6175917
|
TT/CT
|
0.74
|
0.26
|
TT/CT
|
0.74
|
0.26
|
|
S14_6596440
|
6596440
|
TT/TA
|
0.74
|
0.26
|
TT/TA
|
0.74
|
0.26
|
|
S14_7684469
|
7684469
|
AA/AG
|
0.74
|
0.26
|
AA/AG
|
0.75
|
0.25
|
|
S14_8894287
|
8894287
|
GG/GT
|
0.75
|
0.25
|
GG/GT
|
0.76
|
0.24
|
|
S14_9154944
|
9154944
|
TT/GT
|
0.76
|
0.24
|
TT/GT
|
0.76
|
0.24
|
|
S14_9705369
|
9705369
|
TT/CT
|
0.76
|
0.24
|
TT/CT
|
0.77
|
0.23
|
|
S14_3076105
|
3076105
|
TT
|
1
|
0
|
TT/TC
|
0.76
|
0.24
|
|
S14_3084705
|
3084705
|
GG
|
1
|
0
|
GG/GT
|
0.77
|
0.23
|
|
S14_3216815
|
3216815
|
CC
|
1
|
0
|
CC/CT
|
0.76
|
0.24
|
|
S14_3256262
|
3256262
|
GG
|
1
|
0
|
GG/GC
|
0.76
|
0.24
|
|
S14_3256274
|
3256274
|
AA
|
1
|
0
|
AA/AT
|
0.76
|
0.24
|
|
S14_3321418
|
3321418
|
CC
|
1
|
0
|
CC/CT
|
0.77
|
0.23
|
|
S14_3596980
|
3596980
|
TT
|
1
|
0
|
TT/TA
|
0.76
|
0.24
|
|
S14_3891954
|
3891954
|
CC
|
1
|
0
|
CC/CT
|
0.77
|
0.23
|
|
S14_4228151
|
4228151
|
TT
|
1
|
0
|
TT/TA
|
0.76
|
0.24
|
|
S14_6003431
|
6003431
|
CC
|
1
|
0
|
CC/CG
|
0.74
|
0.26
|
|
S14_7623091
|
7623091
|
GG
|
1
|
0
|
GG/GA
|
0.75
|
0.25
|
|
S14_7744603
|
7744603
|
AA
|
1
|
0
|
AA/AC
|
0.74
|
0.26
|
|
S14_7776601
|
7776601
|
GG
|
1
|
0
|
GG/GA
|
0.74
|
0.26
|
|
S14_7829543
|
7829543
|
AA
|
1
|
0
|
AA/AG
|
0.73
|
0.27
|
|
S14_7831615
|
7831615
|
CC
|
1
|
0
|
CC/CT
|
0.74
|
0.26
|
|
S14_7939992
|
7939992
|
CC
|
1
|
0
|
CC/CT
|
0.72
|
0.28
|
|
S14_8196757
|
8196757
|
AA
|
1
|
0
|
AA/AG
|
0.72
|
0.28
|
|
S14_8660835
|
8660835
|
GG
|
1
|
0
|
GG/GC
|
0.73
|
0.27
|
|
S14_9036371
|
9036371
|
GG
|
1
|
0
|
GG/GA
|
0.75
|
0.25
|
|
S14_9154939
|
9154939
|
GG
|
1
|
0
|
GG/GA
|
0.75
|
0.25
|
- SNPs validated by Sequenom MassARRAY from 56 F1 individuals were compared with results from the TASSEL GBS data. Based on alignment with the PN40024 reference genome, SNPs from chromosome 14 were selected from position 2062712 to 9705369 for validation. The top section of the table contains 22 SNPs in which genotypes determined by Sequenom MassARRAY closely matched results produced by the TASSEL GBS pipeline. The bottom section lists SNPs genotyped by Sequenom MassARRAY, which did not match with results from the TASSEL GBS pipeline. MF Major Allele Frequency, MAF Minor Allele Frequency.
