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Table 1 Average number of correctly detected simulated differences by NucDiff with different parameter settings and QUAST

From: NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

Difference

Truth

Default

c30

c120

l10

l65

b80

b350

QUAST-like

QUAST

insertion

1650

1634

1634

1634

1634

1634

1632

1634

1634

858

deletion

1719

1678

1678

1678

1677

1678

1679

1676

1674

465

duplication

251

136

122

150

136

136

137

124

136

196

tandem_duplication

60

57

57

57

57

57

60

54

57

57

collapsed_repeat

58

53

53

53

53

53

54

51

53

53

collapsed_tandem_repeat

59

55

55

55

55

55

56

53

55

55

relocation

217

127

142

108

127

127

136

112

127

130

relocation-insertion

13

13

13

13

13

13

13

13

13

13

relocation-insertion_ATGC

13

13

13

13

13

13

13

13

13

13

relocation-inserted_gap

13

13

13

13

13

13

13

13

13

13

relocation-overlap

13

13

13

13

13

13

13

13

13

12

translocation

111

50

57

43

50

50

50

50

50

62

translocation-insertion

13

12

12

12

12

12

12

12

12

13

translocation-insertion_ATGC

13

13

13

13

13

13

13

13

13

13

translocation-inserted_gap

13

13

13

13

13

13

13

13

13

13

translocation-overlap

13

13

13

13

13

13

13

13

13

11

inversion

534

530

530

528

529

530

531

526

530

528

reshuffling

2585

2585

2585

2585

2585

2585

2585

2585

2585

2536

substitution

115

81

81

81

80

81

89

68

81

84

gap

49

46

46

46

46

46

48

46

45

34

inserted_gap

21

21

21

21

21

21

21

21

20

16

mapped_seq

13

10

11

6

10

10

10

10

10

10

unaligned_sequence

13

13

13

13

13

13

13

13

13

13