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Table 2 Comparison of Sanger derived MLST and AGST loci to their respective de novo assembled genome

From: A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

Typing locus

Original Sanger derived allele

Illumina derived allele

Retested Sanger derived allele

Number of bases, likely cause of discrepancy

MLST

    

f adk

1

10

10

9, mislabelled

f gdh

8

34

34

1, editing error

f pdhC

1

547

547

1, editing error

 

14

60

60

1, editing error

eMLST

    

f pykA

9

5

5

35, mislabelled

f ppk

3

17

17

2, editing error

 

12

1

1

19, mislabelled

f pip

2

1

1

6, mislabelled

 

4

19

19

2, editing error

f dhpS

11

87

87

10, mislabelled

 

10

86

86

1, editing error

 

33

42

42

1, editing error

f aspA

8

78

78

6, mislabelled

f gpm

7

11

11

14, mislabelled

f rpiA

1

18

18

2, editing error

f serC

4

56

56

2, editing error

 

29

56

56

20, mislabelled

 

4

5

5

8, mislabelled

 

8

56

56

8, mislabelled

f talA

7

20

20

3, editing error

 

2

6

6

21, mislabelled

Antigens

    

PorA VR1

7

18-1

18-1

30, mislabelled

PorA VR2

1-1

1-2

1-2

3, mislabelled

 

16

3

3

30, mislabelled

 

15

15-1

15-1

1, editing error

 

14-1

14

14

3, repeat sequence*

fHpb

25

5

5

198, mislabelled

 

39

16

16

5, mislabelled

 

24

14

14

196, mislabelled

 

5

22

22

5, mislabelled

 

35

32

32

51, mislabelled

  1. *repeat sequence compression during assembly; this occurred in 4 different isolates.