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Table 5 Nucleotide diversity, selection pressure, and neutrality tests of the LT-Ag genes and two domains of the PyV groups

From: Codon usage patterns of LT-Ag genes in polyomaviruses from different host species

 Genetic variabilityNeutrality testsSelection pressure
RegionGroupmnSηkπTajima’s DFu and Li’s DFu and Li’s FdN/dS
LT-AgAll869448372129418.2450.44306−0.04390ns1.45113ns0.96702ns2.163
Group A9172512832383737.8890.42776−0.82814ns0.0858ns−0.15345ns0.282
Group F3165712091522910.3330.54939NANANA0.684
Group H13164813362725725.1920.44004−0.80590ns0.16114ns−0.11521ns1.673
Group M36140412052813615.9890.43874−0.35097ns0.89680ns0.54139ns0.523
Group P25160212682653666.1470.41582− 0.20916ns0.88010ns0.62234ns0.318
DnaJ domainAll5416014435271.2040.44503−0.28170ns1.14715ns0.71186ns0.261
Group A916211921468.0830.42027−0.70347ns0.14282ns−0.07065ns0.298
Group H719214623782.1430.42783−0.88626ns−0.18339ns− 0.37879ns0.417
Group M1916213627763.4740.39181−0.83778ns0.31536ns−0.03513ns0.289
Group P1919215329178.5850.4093−0.23632ns0.71490ns0.50101ns0.262
Helicase domainAll86424348827165.8670.39120.02756ns1.22733ns0.85387ns0.316
Group A9471288499159.3610.33835−0.68870ns0.11803ns−0.08782ns0.150
Group F34532853452100.46358NANANA0.379
Group H13477326632174.6670.36618−0.65740ns0.21440ns−0.02451ns0.260
Group M36447346738170.8760.38227−0.15171ns0.86494ns0.60171ns0.503
Group P25471317619161.560.34301−0.05815ns0.97206ns0.75361ns0.142
  1. m, number of sequences used; n, total number of sites (excluding sites with gaps/missing data); S, number of segregating sites; η, total number of mutations; k, average number of pairwise nucleotide differences; π, nucleotide diversity; dS, average number of synonymous substitutions per site; dN, average number of non-synonymous substitutions per site; NA, not available due to limited sequences for analysis of the gene-specific sequence dataset; ns, not significant