Skip to main content

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.