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. 2010 May 21;192(14):3735–3746. doi: 10.1128/JB.00234-10

TABLE 1.

Measures of sequence diversity in the collection of 113 S. pyogenes strains

Gene(s) and strains θb Maximum % divergencec πd πae πsf πa/πsg Ka/Ksh Hdi
Housekeeping genesa
    All strains 0.0076 2.0 0.0074 ± 0.00023 0.0025 0.023 0.105 0.047 0.999 ± 0.001
    NADase-active strains 0.0062 1.9 0.0072 ± 0.00032 0.0024 0.023 0.102 0.047 0.998 ± 0.004
    NADase-inactive strains 0.0057 1.7 0.0075 ± 0.00033 0.0026 0.023 0.108 0.047 0.999 ± 0.004
spn
    All strains 0.0068 2.9 0.0079 ± 0.004 0.0045 0.019 0.256 0.23 0.987 ± 0.004
    NADase-active strains 0.0059 2.7 0.0097 ± 0.00051 0.0052 0.026 0.202 0.209 0.977 ± 0.01
    NADase-inactive strains 0.0042 1.6 0.0075 ± 0.00037 0.0032 0.012 0.256 0.294 0.981 ± 0.008
ifs
    All strains 0.0099 2.5 0.0094 ± 0.00038 0.0090 0.010 0.906 0.644 0.961 ± 0.006
    NADase-active strains 0.0056 2.1 0.0069 ± 0.00055 0.0051 0.013 0.386 0.444 0.908 ± 0.02
    NADase-inactive strains 0.0074 1.9 0.0060 ± 0.00065 0.0059 0.004 1.314 0.838 0.923 ± 0.019
a

Housekeeping genes include the concatenated sequences from the internal fragments of gki, gtr, murL, mutS, recP, xpt, and yqiL.

b

θ is the average number of nucleotide differences per nucleotide site (calculated using DnaSP v5.0).

c

The maximum percent divergence is the number of polymorphic nucleotide sites between the two most dissimilar sequences in the population divided by the length of the gene (calculated using MegAlign in DNASTAR Lasergene 8 after a ClustalW alignment).

d

π is the average pairwise nucleotide diversity (calculated using DnaSP v5.0).

e

πa is the average pairwise nucleotide diversity leading to nonsynonymous mutations (calculated using DnaSP v5.0).

f

πs is the average pairwise nucleotide diversity leading to synonymous mutations (calculated using DnaSP v5.0).

g

πa/πs is the ratio of nonsynonymous to synonymous mutations (calculated using DnaSP v5.0).

h

Ka/Ks is the ratio of the rate of nonsynonymous to synonymous mutations (calculated using DnaSP v5.0).

i

Haplotype diversity (Hd) is the probability that two sequences selected at random from the sample population will be different (calculated using DnaSP v5.0).