| |
na
|
Genotype concordance (%)
|
Allele concordance (%)
|
Concordance by genotype (%)
|
|---|
|
True = 0
|
True = 1
|
True = 2
|
|---|
|
0|0
|
1|0
|
2|0
|
0|1
|
1|1
|
2|1
|
0|2
|
1|2
|
2|2
|
|---|
|
Low coverage
|
|
1×
|
27,185
|
42.2
|
61.0
|
99.97
|
–
|
0.03
|
95.14
|
–
|
4.86
|
81.96
|
–
|
18.04
|
|
2×
|
33,638
|
57.2
|
76.0
|
99.94
|
0.00
|
0.06
|
72.87
|
3.51
|
23.62
|
20.07
|
0.25
|
79.68
|
|
3×
|
24,789
|
70.3
|
84.5
|
99.91
|
0.08
|
0.01
|
56.37
|
31.87
|
11.76
|
6.23
|
1.45
|
92.32
|
|
4×
|
14,015
|
79.7
|
89.6
|
99.85
|
0.13
|
0.02
|
43.11
|
51.44
|
5.46
|
2.14
|
1.69
|
96.16
|
|
5×
|
6502
|
85.6
|
92.7
|
99.93
|
0.04
|
0.04
|
32.65
|
64.75
|
2.59
|
0.90
|
1.96
|
97.14
|
|
6–10×
|
3705
|
90.5
|
95.2
|
99.83
|
0.12
|
0.06
|
22.47
|
74.68
|
2.85
|
0.61
|
1.07
|
98.32
|
|
Overall
|
109,834
|
62.1
|
77.6
|
99.92
|
0.04
|
0.03
|
66.41
|
21.50
|
12.09
|
29.84
|
0.71
|
69.45
|
|
High coverage
|
131,806
|
99.7
|
99.9
|
99.80
|
0.19
|
0.01
|
0.21
|
99.72
|
0.07
|
0.17
|
0.16
|
99.68
|
- aNumber of genotypes called across 26 individuals at 5136 and 5531 SNPs for low- and high-coverage data, respectively
- Concordance is shown by coverage at variant site
