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Table 4 Variant detection in coding and none coding regions of the four analyzed VHSV genomes.

From: Ultra-deep sequencing of VHSV isolates contributes to understanding the role of viral quasispecies

Reference genome

DK-3592b (Acc No KC778774)

FA281107 (Acc No EU481506)

Isolate

DK-3592b

DK-9895174

1p49

4p168

Filtering

Nt

Aa

Nt, Q

Aa, Q

Nt, QF

Aa, QF

Nt

Aa

Nt, Q

Aa, Q

Nt, QF

Aa, QF

Nt

Aa

Nt, Q

Aa, Q

Nt, QF

Aa, QF

Nt

Aa

Nt, Q

Aa, Q

Nt, QF

Aa, QF

Leader

4

–

0

–

0

–

7

–

0

–

0

–

12

–

0

–

0

–

0

–

0

–

0

–

N

7

1

5

0

2

0

15

3

12

1

0

0

200

33

94

15

0

0

14

8

10

7

0

0

Inter N-P

3

–

1

–

0

–

3

–

2

–

0

–

11

–

6

–

0

–

0

–

0

–

0

–

P

2

1

3

1

0

0

17

4

17

3

0

0

72

11

48

7

0

0

5

2

5

2

0

0

Inter P-M

2

–

0

–

0

–

3

–

1

–

0

–

26

–

8

–

0

–

6

–

5

–

0

–

M

2

1

0

0

0

0

13

5

6

2

0

0

88

18

29

5

0

0

9

3

6

1

0

0

Inter M-G

0

–

0

–

0

–

1

–

1

–

0

–

20

–

11

–

0

–

5

–

4

–

0

–

G

22

9

17

4

5

1

60

27

48

22

9

4

286

45

161

16

7

1

32

7

15

3

2

1

Inter G-Nv

6

–

0

–

0

–

5

–

3

–

0

–

17

–

13

–

0

–

0

–

5

–

0

–

Nv

20

9

12

1

0

0

23

12

22

11

0

0

65

33

37

18

2

0

11

4

5

3

1

0

Inter Nv-L

4

–

0

–

0

–

6

–

5

–

0

–

11

–

8

–

0

–

2

–

1

–

0

–

L

15

1

8

0

3

0

85

10

65

5

0

0

869

73

464

32

91

4

51

12

38

5

0

0

Trailera

0

–

0

–

0

–

0

–

0

–

0

–

0

–

0

–

0

–

0

–

0

–

0

–

Total

87

22

46

6

10

1

238

61

182

44

9

4

1677

213

879

93

100

5

135

36

94

21

3

1

  1. The table summarizes the distribution of nucleotide (Nt) and amino acid (Aa) variants before and after filtering procedures. Two filtering procedures were applied based on read quality (Q) and variant frequency at polymorphic sites (F). Read quality filtering was applied using the following parameters: equality in forward and reverse reads should be at least 0.35, average quality at least 30, while statistical testing of read position- as well as read direction probability should exceed 10−12. Filtering on variant frequency was conducted to distinguish true variants from errors introduced during sequence preparation and sequencing. Only polymorphic sites with variants with intermediate allel frequencies (5–95%) were incluede whereas polymorphic sites with minor allele frequencies below 5% were excluded from analysis.
  2. aCoverage of trailer was below 80×.
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