Virology Journal

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 variability				Neutrality tests			Selection pressure
Region	Group	m	n	S	η	k	π	Tajima’s D	Fu and Li’s D	Fu and Li’s F	dN/dS
LT-Ag	All	86	944	837	2129	418.245	0.44306	−0.04390^ns	1.45113^ns	0.96702^ns	2.163
	Group A	9	1725	1283	2383	737.889	0.42776	−0.82814^ns	0.0858^ns	−0.15345^ns	0.282
	Group F	3	1657	1209	1522	910.333	0.54939	NA	NA	NA	0.684
	Group H	13	1648	1336	2725	725.192	0.44004	−0.80590^ns	0.16114^ns	−0.11521^ns	1.673
	Group M	36	1404	1205	2813	615.989	0.43874	−0.35097^ns	0.89680^ns	0.54139^ns	0.523
	Group P	25	1602	1268	2653	666.147	0.41582	− 0.20916^ns	0.88010^ns	0.62234^ns	0.318
DnaJ domain	All	54	160	144	352	71.204	0.44503	−0.28170^ns	1.14715^ns	0.71186^ns	0.261
	Group A	9	162	119	214	68.083	0.42027	−0.70347^ns	0.14282^ns	−0.07065^ns	0.298
	Group H	7	192	146	237	82.143	0.42783	−0.88626^ns	−0.18339^ns	− 0.37879^ns	0.417
	Group M	19	162	136	277	63.474	0.39181	−0.83778^ns	0.31536^ns	−0.03513^ns	0.289
	Group P	19	192	153	291	78.585	0.4093	−0.23632^ns	0.71490^ns	0.50101^ns	0.262
Helicase domain	All	86	424	348	827	165.867	0.3912	0.02756^ns	1.22733^ns	0.85387^ns	0.316
	Group A	9	471	288	499	159.361	0.33835	−0.68870^ns	0.11803^ns	−0.08782^ns	0.150
	Group F	3	453	285	345	210	0.46358	NA	NA	NA	0.379
	Group H	13	477	326	632	174.667	0.36618	−0.65740^ns	0.21440^ns	−0.02451^ns	0.260
	Group M	36	447	346	738	170.876	0.38227	−0.15171^ns	0.86494^ns	0.60171^ns	0.503
	Group P	25	471	317	619	161.56	0.34301	−0.05815^ns	0.97206^ns	0.75361^ns	0.142

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

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ISSN: 1743-422X

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