Table 1

Properties and diversities of MLST and AA-MLST loci
Locus Fragment sizeA Number and proportion of allelesB Number and proportion of new alleles Number and proportion of variable sitesB D Simpsons Index of diversityB dN/dS ratioBC
MLST AA-MLST MLST AA-MLST MLST AA-MLST MLST AA-MLST MLST AA-MLST MLST
dnaE 555 bp 185 aa 55; 14.8% (195; 13.7%) 5; 12.8% (15; 10.6%) 13; 23.6% 2; 40.0% 55; 9.9% (115; 20.7%) 3; 1.6% (11; 5.9%) 0.988 (0.985) 0.630 (0.614) 0.026 (0.025)
gyrB 591 bp 197 aa 65; 17.5% (274; 19.2%) 1; 2.6% (7; 4.9%) 28; 43.1% 0; 0.0% 47; 8.0% (100; 16.9%) *; - (6; 3.0%) 0.992 (0.989) 0.000 (0.094) 0.000 (0.002)
recA 726 bp 242 aa 57; 15.3% (201; 14.1%) 1; 2.6% (9; 6.3%) 21; 36.8% 0; 0.0% 66; 9.1% (216; 29.8%) *; - (24; 9.9%) 0.987 (0.985) 0.000 (0.106) 0.006 (0.015)
dtdS 456 bp 152 aa 55; 14.8% (237; 16.6%) 3; 7.7% (9; 6.3%) 17; 36.4% 1; 33.3% 50; 11.0% (100; 21.9%) 2; 1.3% (8; 5.3%) 0.983 (0.987) 0.127 (0.117) 0.002 (0.002)
pntA 429 bp 143 aa 41; 11.0% (146; 10.3%) 7; 17.9% (36; 25.4%) 11; 26.8% 4; 57.1% 41; 9.6% (85; 19.8%) 6; 4.2% (29; 20.8%) 0.965 (0.966) 0.404 (0.525) 0.018 (0.042)
pyrC 489 bp 163 aa 55; 14.8% (219; 15.4%) 14; 35.9% (41; 28.9%) 20; 38.2% 3; 21.4% 48; 9.8% (107; 21.8%) 11; 6.8% (31; 19.0%) 0.986 (0.981) 0.791 (0.753) 0.045 (0.049)
tnaA 423 bp 141 aa 44; 11.8% (152; 10.7%) 8; 20.5% (25; 17.6%) 15; 34.1% 4; 50.0% 41; 9.7% (89; 21.0%) 6; 4.3% (22; 15.6%) 0.974 (0.97) 0.355 (0.440) 0.019 (0.023)
total 3669 bp 1223 aa 372; 100% (1424; 100%) 39; 100% (142; 100%) 125; 33.6% 15; 29.9% 348; 9.5% (812; 22.1%) 28; 2.3% (131; 10.7%)

Ain-frame fragment size.

BValues in parentheses are computed based on the data of the entire pubMLST dataset.

CdN/dS ratio, ratio of non-synonymous to synonymous mutations, value <1 indicates purifying selection of loci.

*For the one occurring allele no variable sites could be determined.

Urmersbach et al.

Urmersbach et al. BMC Microbiology 2014 14:59   doi:10.1186/1471-2180-14-59

Open Data