|
Percentage
|
Method
|
Var calls
|
cov(fold)
|
cov(%)
|
refCall/ Δ
|
|---|
|
1
|
NoRMDup
|
1
|
1.16
|
1.02
|
33,277
|
|
1
|
DeDup
|
1
|
1.16
|
1.01
|
−207
|
|
1
|
rmdup
|
1
|
1.16
|
0.98
|
−1,362
|
|
2
|
NoRMDup
|
11
|
2.33
|
10.17
|
332,395
|
|
2
|
DeDup
|
11
|
2.33
|
10.14
|
−1,051
|
|
2
|
rmdup
|
11
|
2.32
|
9.85
|
−10,563
|
|
4
|
NoRMDup
|
55
|
4.7
|
49.82
|
1,628,172
|
|
4
|
DeDup
|
55
|
4.69
|
49.73
|
−2,978
|
|
4
|
rmdup
|
55
|
4.64
|
49.10
|
−23,481
|
|
5
|
NoRMDup
|
80
|
5.89
|
66.85
|
2,184,874
|
|
5
|
DeDup
|
80
|
5.88
|
66.77
|
−2,889
|
|
5
|
rmdup
|
78
|
5.8
|
66.19
|
−21,761
|
|
6
|
NoRMDup
|
91
|
7.06
|
78.85
|
2,576,795
|
|
6
|
DeDup
|
91
|
7.05
|
78.78
|
−2,219
|
|
6
|
rmdup
|
89
|
6.94
|
78.31
|
−17,500
|
|
7
|
NoRMDup
|
102
|
8.26
|
86.68
|
2,832,796
|
|
7
|
DeDup
|
102
|
8.24
|
86.62
|
−1,931
|
|
7
|
rmdup
|
101
|
8.09
|
86.29
|
−12,650
|
|
70
|
NoRMDup
|
114
|
82.58
|
98.39
|
3,215,440
|
|
70
|
DeDup
|
114
|
80.84
|
98.39
|
0
|
|
70
|
rmdup
|
114
|
68.87
|
98.39
|
−52
|
|
80
|
NoRMDup
|
114
|
94.38
|
98.4
|
3,215,840
|
|
80
|
DeDup
|
114
|
92.11
|
98.4
|
−2
|
|
80
|
rmdup
|
114
|
76.89
|
98.4
|
−54
|
|
90
|
NoRMDup
|
114
|
106.23
|
98.42
|
3,216,400
|
|
90
|
DeDup
|
114
|
103.36
|
98.42
|
0
|
|
90
|
rmdup
|
114
|
84.62
|
98.42
|
−30
|
|
100
|
NoRMDup
|
114
|
118.03
|
98.43
|
3,216,748
|
|
100
|
DeDup
|
114
|
114.51
|
98.43
|
−1
|
|
100
|
rmdup
|
114
|
92.02
|
98.43
|
−30
|
- The first column describes the percentage of randomly drawn reads from the Jorgen625 leprosy data set, with a genome size of 3,268,202 base pairs. Var calls shows the number of variant positions that were called. cov(fold) and cov(%) show the coverage of the genome. refCall describes the number of reference calls that were made, where Δ describes the difference between the non-de-duplicated sample at the given sub-sampling degree and the duplicate removed sample. All other positions of the genome have been filtered out. The parameters to call a position confidently were a coverage of at least fivefold, a variant quality of at least 30, and a minimum allele frequency of 90 %. NoRMDup refers to not applying any duplicate removal to the corresponding sample
