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Table 2 Genetic diversity and neutrality test statistics by lineage (L1-L4)

From: Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999–2009

Lineage N S π D T D FL F FL R 2 H FW Hn FW
L1 7 2238 1.7E-4 −1.157 −0.9802 (−1.7817*) −1.0910 (−1.9267*) 0.0812** 457.62 1.180
L2 9 2240 1.3E-4 −1.627 −1.66780 (−2.3468**) −1.8172 (−2.5742**) 0.0795** 162.92 0.430
L1/L2/L3 19 6249 2.7E-4 −1.622 −2.1420* (−2.9363**) −2.2253* (−2.9868**) 0.0631** 635.80 0.671
L4 47 4892 1.1E-4 −2.205* −4.3046** (−5.3287**) −4.1559** (−4.8682**) 0.0334** 304.47 0.490
L4: NYC 21 2262 8.9E-5 −1.649 −2.5102* (−3.3684 *) −2.6277* (−3.4054 *) 0.0593** 230.01 0.7874
L4: S75 9 149 1.5E-5 −0.498 0.07218 (0.45497) −0.07462 (0.22079) 0.1297 −29.14 −1.125
  1. N, number of ingroup sequences; S, number of segregating sites; π, nucleotide diversity; k, average number of nucleotide differences; D T , Tajima’s D; R 2 , Ramos-Onsins and Rozas’ R 2 , D FL and F FL , Fu and Li’s D and F (calculated with M. bovis as an outgroup); H FW , Fay and Wu’s H; Hn FW , Fay and Wu’s normalized H. Statistical significance was assess with 10,000 coalescent simulations (50,000 simulations for R 2 ). *P < 0.05, **P < 0.005