|
All allele frequencies
|
≤5% MAF
|
2% MAF(4 alleles in pool)
|
0.5% MAF(1 allele in pool)
|
---|
Size Multiplex
|
Coverage
|
Percent of Bases, average (SD)
|
Homozygous wild type sites
|
Heterozygous sites
|
Homozygous variant sites
|
Sensitivity average (SD)
|
Specificity, average (SD)
|
Homozygous wild-type sites
|
Heterozygous sites
|
Homozygous variant sites
|
Sensitivity (avg)
|
Specificity (avg)
|
Heterozygous sites
|
Sensitivity (avg)
|
Specificity (avg)
|
Heterozygous sites
|
Sensitivity (avg)
|
Specificity (avg)
|
---|
22-24
|
≥3
|
84.4(1.29)
|
229483
|
39100
|
24855
|
95.02(1.42)
|
99.82(0.14)
|
172205
|
2057
|
20
|
92.49
|
99.98
|
656
|
91.6
|
99.98
|
127
|
88.3
|
99.99
|
|
≥5
|
84.6(1.75)
|
221031
|
37332
|
23810
|
96.75(1.23)
|
99.82(0.14)
|
166050
|
1961
|
19
|
95.30
|
99.98
|
624
|
94.9
|
99.99
|
119
|
90.2
|
99.99
|
|
≥10
|
75.0(2.65)
|
201268
|
33626
|
21451
|
98.22(0.98)
|
99.86(0.13)
|
151395
|
1768
|
17
|
97.42
|
99.98
|
563
|
96.6
|
99.99
|
111
|
93.8
|
100
|
|
≥15
|
67.1(3.57)
|
182332
|
30279
|
19510
|
98.60(0.93)
|
99.88(0.12)
|
137327
|
1579
|
17
|
98.50
|
99.98
|
507
|
98.0
|
99.99
|
100
|
96.0
|
100
|
|
≥20
|
59.8(4.51)
|
163986
|
27202
|
17643
|
98.94(0.83)
|
99.89(0.12)
|
123572
|
1418
|
14
|
98.81
|
99.98
|
460
|
98.7
|
100
|
90
|
95.6
|
100
|
48
|
≥3
|
89.0(2.30)
|
239300
|
39218
|
26310
|
95.80(1.42)
|
99.90(0.08)
|
187077
|
2109
|
25
|
92.97
|
99.97
|
651
|
92.9
|
99.99
|
131
|
94.7
|
100
|
|
≥5
|
84.1(3.14)
|
230685
|
37434
|
25232
|
96.43(0.95)
|
99.91(0.08)
|
179900
|
1997
|
25
|
95.95
|
99.97
|
619
|
95.8
|
99.99
|
125
|
96.8
|
100
|
|
≥10
|
74.8(4.54)
|
209960
|
33448
|
22739
|
98.96(0.51)
|
99.94(0.07)
|
163128
|
1805
|
22
|
98.30
|
99.97
|
566
|
98.4
|
99.99
|
111
|
100
|
100
|
|
≥15
|
67.1(5.79)
|
190652
|
30010
|
20491
|
99.33(0.42)
|
99.95(0.07)
|
147843
|
1630
|
19
|
98.85
|
99.97
|
517
|
99.0
|
99.99
|
100
|
100
|
100
|
|
≥20
|
60.3(6.98)
|
172373
|
26937
|
18505
|
99.60(0.37)
|
99.96(0.06)
|
133259
|
1449
|
18
|
99.05
|
99.97
|
467
|
99.6
|
100
|
88
|
100
|
100
|
30-32
|
≥3
|
89.2(2.55)
|
245952
|
40732
|
26487
|
96.52(1.08)
|
99.97(0.03)
|
184498
|
1903
|
16
|
93.54
|
99.97
|
664
|
95.6
|
99.98
|
102
|
97.1
|
99.99
|
|
≥5
|
84.4(3.49)
|
235796
|
38696
|
25251
|
98.23(0.69)
|
99.97(0.03)
|
177279
|
1809
|
16
|
96.33
|
99.97
|
644
|
97.1
|
99.99
|
102
|
97.1
|
100
|
|
≥10
|
74.8(5.35)
|
212716
|
34440
|
22505
|
99.43(0.40)
|
99.97(0.03)
|
160352
|
1600
|
14
|
98.88
|
99.97
|
567
|
99.1
|
99.99
|
99
|
96.8
|
100
|
|
≥15
|
66.8(7.25)
|
192642
|
30957
|
20272
|
99.80(0.19)
|
99.98(0.03)
|
145504
|
1403
|
12
|
99.58
|
99.98
|
497
|
99.4
|
100
|
82
|
97.6
|
100
|
|
≥20
|
59.5(9.08)
|
173212
|
27775
|
18237
|
99.90(0.15)
|
99.98(0.03)
|
130959
|
1260
|
10
|
99.76
|
99.98
|
448
|
99.6
|
100
|
72
|
98.8
|
100
|
- The percent of bases in the targeted intervals that reached the specified coverage threshold is listed. Homozygous wild type, heterozygous, and homozygous variant sites surveyed indicates the number of each of those positions as seen by the Illumina Omni 2.5-8 array that were used to determine sensitivity and specificity. Sensitivity is the percentage of heterozygous and homozygous variant sites correctly called heterozygous and homozygous variant, respectively. Specificity is the percentage of homozygous wild type sites called as homozygous wild type. For “All allele frequencies” these values were averaged among all non-excluded samples. For ≤5%, 2% and 0.5% minor allele frequencies, these values were determined from the cumulative metrics of all non-excluded samples at sites with 9 or fewer, 4 or fewer, or 1 variant allele in the entire pool, respectively.