|
Conventional-primer method
| |
|---|
| |
Concordant
|
Discordant
|
Concordance (%)b
|
|---|
|
Chr
|
Position
|
Ref
|
Alt
|
MMb
|
Mmb
|
mmb
|
MM
|
Mm
|
mm
| |
|
5
|
124968560
|
C
|
T
|
0
|
11
|
5
|
0
|
0
|
0
|
|
6
|
120556623
|
T
|
C
|
1
|
8
|
0
|
0
|
0
|
0
|
|
7
|
25377202
|
A
|
G
|
0
|
2
|
1
|
0
|
0
|
0
|
|
12
|
81073590
|
G
|
T
|
5
|
4
|
0
|
0
|
0
|
0
|
|
17
|
4536929
|
G
|
A
|
2
|
8
|
0
|
0
|
0
|
0
|
|
18
|
11257808
|
A
|
G
|
2
|
8
|
0
|
0
|
0
|
0
|
|
18
|
63490716
|
C
|
T
|
6
|
17
|
0
|
0
|
0
|
0
|
|
23
|
18485367
|
C
|
G
|
2
|
8
|
0
|
0
|
0
|
0
|
|
28
|
1121069
|
G
|
T
|
5
|
5
|
0
|
0
|
0
|
0
|
| |
Total
|
23
|
71
|
6
|
0
|
0
|
0
|
100.0
|
|
Selective-primer method
|
|
5
|
124968560
|
C
|
T
|
3
|
13
|
16
|
0
|
9
|
0
| |
|
6
|
120556623
|
T
|
C
|
10
|
22
|
12
|
0
|
2
|
0
|
|
7
|
25377202
|
A
|
G
|
5
|
17
|
19
|
0
|
1
|
1
|
|
11
|
6123151
|
T
|
C
|
18
|
13
|
3
|
0
|
8
|
0
|
|
12
|
81073590
|
G
|
T
|
19
|
11
|
3
|
0
|
7
|
0
|
|
17
|
4536929
|
G
|
A
|
11
|
11
|
12
|
0
|
9
|
0
|
|
18
|
11257808
|
A
|
G
|
20
|
16
|
6
|
0
|
3
|
0
|
|
18
|
63490716
|
C
|
T
|
17
|
13
|
4
|
0
|
7
|
0
|
|
23
|
18485367
|
C
|
G
|
18
|
13
|
2
|
0
|
4
|
0
|
|
24
|
26394985
|
G
|
T
|
18
|
13
|
7
|
0
|
5
|
0
|
|
24
|
26395035
|
C
|
T
|
7
|
14
|
18
|
0
|
6
|
0
|
|
28
|
1121069
|
G
|
T
|
24
|
9
|
0
|
0
|
6
|
0
|
|
X
|
49928152
|
C
|
T
|
34
|
8
|
0
|
0
|
0
|
0
|
| |
Total
|
204
|
173
|
102
|
0
|
68
|
0
|
87.6
|
-
aThe 13 single-nucleotide polymorphisms (SNPs) examined were initially detected in a selective-primer dataset. Only 9 of these 13 SNPs could be retrieved in the corresponding conventional-primer dataset. Variants in these datasets were kept if they qualified based on a read depth ≥ 5, a genotype quality score ≥ 20, no more than one alternative allele, a call rate > 0.2, and a minor allele frequency ≥ 0.025. Chr: chromosome; Ref: reference allele; Alt: alternate allele; MM: homozygous for the reference allele; Mm: heterozygous; mm: homozygous for the alternate allele
-
bThe reliability of SNP prediction was based on the reference calls predicted using the Sequenom MassARRAY technology. Discordant SNP reports call conflict by GBS
