Table 1 Genomic features and Predicted insertion sequence elements of S. flexneri (FC906) and S. sonnei (FC1653) by hybrid assembly approach

Genomic features

 Length

4,655,489 bp

4,807,231 bp

 Coverage

278×

174×

 Contigs

1 (chromosome)

4 (1 chromosome, 3 plasmid)

 Total genes

4770

4932

 Total CDS

4637

4806

 Total pseudo genes

735

857

 tRNAs

104

95

 rRNAs

22

22

 GC content

50.8

51.0

 Virulence factor (VFDB)

66

57

 Resistance (CARD)

90

86

 Sequence type

245

152

Insertion sequence elements predicted using ISsaga

 IS4_ssgr_IS4

[2/42/0/0]

1

44

[1/85/0/0]

1

86

 ISL3

[0/1/0/3]

4

4

[0/0/0/1]

1

1

 ISNCY_ssgr_ISPlu15

[4/0/0/0]

4

4

[2/1/0/2]

5

5

 IS4_ssgr_IS50

[0/0/0/1]

1

1

[0/0/0/1]

1

1

 IS3_ssgr_IS3

[45/126/0/0]

4

105

[26/132/0/1]

1

94

 IS1

[107/14/0/0]

2

114

[119/60/0/0]

2

172

 IS66

[6/22/0/0]

2

14

[3/3/0/0]

1

2

 IS3_ssgr_IS150

[2/3/0/0]

1

3

[0/1/0/0]

1

1

 IS200_IS605

[0/6/0/0]

2

6

[0/4/0/0]

2

4

 IS91

[0/11/0/0]

3

11

[1/0/0/0]

1

1

 IS3_ssgr_IS2

[22/52/0/0]

1

44

[26/46/0/0]

2

45

 IS3_ssgr_IS51

[19/31/0/1]

2

32

[5/6/0/1]

2

7

 IS110_ssgr_IS1111

[1/0/0/0]

1

1

[5/11/0/0]

2

16

 IS110

[3/2/0/0]

1

5

[1/13/0/0]

1

14

 ISAs1

–

–

–

[2/5/0/0]

1

7

 IS21

–

–

–

[13/68/0/0]

2

50

 IS630

–

–

–

[1/28/0/0]

1

29

 IS256

[0/1/0/0]

1

1

–

–

–

 Tn3

[1/0/0/0]

1

1

–

–

–

 IS4_ssgr_IS10

[1/0/0/0]

1

1

–

–

–