| |
na
|
Genotype concordance (%)
|
Allele concordance (%)
|
Concordance by genotype (%)
|
|---|
|
True = 0
|
True = 1
|
True = 2
|
|---|
|
0|0b
|
1|0
|
2|0
|
0|1
|
1|1
|
2|1
|
0|2
|
1|2
|
2|2
|
|---|
|
Best-guess
|
|
1×
|
30,875
|
62.6
|
81.1
|
99.45
|
–
|
0.55
|
51.35
|
–
|
48.65
|
0.70
|
–
|
99.30
|
|
2×
|
35,688
|
79.9
|
90.0
|
98.60
|
1.40
|
0.00
|
26.20
|
48.26
|
25.54
|
0.04
|
1.61
|
98.35
|
|
3×
|
28,357
|
88.6
|
94.3
|
98.36
|
1.64
|
0.00
|
13.80
|
72.20
|
14.00
|
0.00
|
2.22
|
97.78
|
|
4×
|
17,849
|
92.7
|
96.4
|
98.05
|
1.95
|
0.00
|
8.22
|
84.01
|
7.77
|
0.00
|
2.63
|
97.37
|
|
5×
|
9619
|
95.3
|
97.6
|
97.40
|
2.60
|
0.00
|
4.55
|
91.52
|
3.93
|
0.00
|
2.49
|
97.51
|
|
6–10×
|
7047
|
95.2
|
97.6
|
97.73
|
2.27
|
0.00
|
4.96
|
91.05
|
4.00
|
0.00
|
2.68
|
97.32
|
|
Overall
|
129,435
|
81.4
|
90.7
|
98.53
|
1.34
|
0.13
|
24.27
|
52.40
|
23.33
|
0.18
|
1.61
|
98.21
|
|
Probability ≥ 0.90
|
|
1×
|
0
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
|
2–3×b
|
14,572
|
95.5
|
97.7
|
–
|
100.00
|
–
|
–
|
100.00
|
–
|
–
|
100.00
|
–
|
|
4×
|
14,359
|
92.7
|
96.3
|
99.97
|
0.03
|
0.00
|
16.24
|
68.39
|
15.37
|
0.00
|
0.05
|
99.95
|
|
5×
|
8315
|
96.3
|
98.2
|
99.92
|
0.08
|
0.00
|
6.76
|
87.41
|
5.83
|
0.00
|
0.10
|
99.90
|
|
6–10×
|
6397
|
98.1
|
99.0
|
99.83
|
0.17
|
0.00
|
3.08
|
94.65
|
2.27
|
0.00
|
0.29
|
99.71
|
|
Overall
|
43,643
|
95.1
|
97.5
|
97.18
|
2.82
|
0.00
|
3.52
|
93.26
|
3.21
|
0.00
|
3.65
|
96.35
|
|
Probability ≥ 0.98
|
|
1–3×
|
0
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
–
|
|
4–5×b
|
4366
|
99.8
|
99.9
|
–
|
100.00
|
–
|
–
|
100.00
|
–
|
–
|
100.00
|
–
|
|
6–10×
|
6313
|
98.1
|
99.1
|
99.83
|
0.17
|
0.00
|
3.15
|
94.58
|
2.26
|
0.00
|
0.29
|
99.71
|
|
Overall
|
10,679
|
98.8
|
99.4
|
99.65
|
0.35
|
0.00
|
1.00
|
98.28
|
0.72
|
0.00
|
0.57
|
99.43
|
- aNumber of genotypes called for 5,531 SNPs across 26 individuals
- bHeterozygotes are easier to call than homozygotes; at these coverages, certainty is not sufficient to call the homozygotes, but note, that the actual counts for (1|0) and (1|2) are very low compared to (1|1): 19-fold and 569-fold lower for genotypes called with a probability greater than 0.90 and 0.98, respectively
- Concordance is shown by coverage at variant site
