Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution

Nasrullah, Izza; Butt, Azeem M; Tahir, Shifa; Idrees, Muhammad; Tong, Yigang

doi:10.1186/s12862-015-0456-4

Table 1 Nucleotide composition analysis of MARV coding sequences (%)

From: Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution

No	A	U	G	C	A_3S	U_3S	G_3S	C_3S	AU	GC	GC_1S	GC_2S	AU_3S	GC_3S	GC_12S	ENC	ARO	GRAVY
1	31.9	27.6	19.7	20.8	31.2	32.8	18.1	18	59.5	40.5	46.4	39	64	36.1	42.7	54.76	9	−32
2	32	27.8	19.5	20.7	31.6	33.3	17.4	17.8	59.8	40.2	46.5	38.9	64.9	35.2	42.7	54.96	9	−33
3	32	27.8	19.5	20.6	31.5	33.4	17.4	17.8	59.8	40.2	46.5	38.9	64.9	35.1	42.7	53.54	9	−32
4	32	27.7	19.5	20.7	31.5	33.2	17.4	17.9	59.7	40.3	46.5	38.9	64.7	35.3	42.7	53.59	9	−33
5	32	27.7	19.6	20.8	31.5	33.2	17.4	18	59.7	40.3	46.6	39	64.7	35.3	42.8	53.59	9	−33
6	32	27.8	19.5	20.6	31.5	33.4	17.4	17.8	59.8	40.2	46.5	38.9	64.9	35.1	42.7	53.57	9	−32
7	32	27.6	19.5	20.9	31.4	33	17.5	18.1	59.6	40.4	46.4	39	64.4	35.6	42.7	53.66	9	−32
8	32	27.7	19.5	20.8	31.4	33	17.6	18	59.7	40.4	46.5	39.1	64.4	35.6	42.8	53.64	9	−33
9	32	27.8	19.6	20.6	31.5	33.4	17.3	17.7	59.8	40.2	46.6	38.9	64.9	35.1	42.75	54.67	9	−33
10	32	27.6	19.5	20.9	31.4	32.9	17.5	18.2	59.6	40.4	46.5	39.1	64.3	35.7	42.8	54.17	9	−33
11	31.9	27.5	19.7	20.9	31.2	32.6	18	18.2	59.4	40.6	46.6	38.8	63.8	36.3	42.7	53.43	9	−32
12	31.9	27.7	19.6	20.8	31.2	33.2	17.7	17.9	59.6	40.4	46.4	39.1	64.4	35.6	42.75	54.64	9	−33
13	31.9	27.7	19.6	20.8	31.2	33.2	17.6	17.9	59.6	40.3	46.4	39.1	64.4	35.5	42.75	54.47	9	−33
14	32	27.7	19.5	20.8	31.4	33	17.6	18	59.7	40.4	46.5	39.1	64.4	35.6	42.8	54.29	9	−33
15	32	27.7	19.5	20.8	31.4	33	17.5	18	59.7	40.3	46.4	39	64.4	35.5	42.7	54.14	9	−33
16	32	27.6	19.5	20.8	31.4	33	17.5	18.1	59.6	40.3	46.4	39	64.4	35.6	42.7	53.91	9	−33
17	32	27.7	19.5	20.8	31.3	33.1	17.6	18	59.7	40.4	46.5	39.1	64.4	35.6	42.8	54.31	9	−33
18	32	27.6	19.5	20.8	31.4	33	17.5	18	59.6	40.3	46.4	39	64.4	35.6	42.7	54.36	9	−33
19	32	27.7	19.5	20.8	31.4	33	17.5	18	59.7	40.3	46.4	39	64.4	35.5	42.7	54.31	9	−33
20	32	27.7	19.5	20.8	31.4	33	17.5	18	59.7	40.3	46.4	39	64.4	35.5	42.7	54.33	9	−33
21	32	27.6	19.5	20.8	31.4	33	17.5	18.1	59.6	40.3	46.4	39	64.4	35.6	42.7	54.31	9	−33
22	32	27.7	19.5	20.8	31.3	33.2	17.6	17.9	59.7	40.3	46.5	39.1	64.5	35.5	42.8	54.39	9	−33
23	32	27.6	19.5	20.8	31.4	33	17.5	18	59.6	40.3	46.4	39	64.4	35.5	42.7	54.27	9	−33
24	32	27.6	19.5	20.9	31.4	33	17.5	18.1	59.6	40.3	46.4	39	64.4	35.6	42.7	54.34	9	−33
25	32	27.6	19.5	20.9	31.4	33	17.5	18.1	59.6	40.4	46.5	39	64.4	35.6	42.75	54.30	9	−33
26	32	27.7	19.5	20.9	31.3	32.9	17.7	18.1	59.7	40.4	46.4	39	64.2	35.8	42.7	54.63	9	−33
27	32	27.7	19.5	20.9	31.3	32.9	17.7	18.1	59.7	40.4	46.4	39	64.2	35.8	42.7	54.63	9	−33
28	32	27.6	19.5	20.9	31.3	33	17.6	18.1	59.6	40.3	46.3	39	64.3	35.7	42.65	54.37	9	−33
29	32	27.6	19.5	20.9	31.4	33	17.5	18.1	59.6	40.3	46.4	39	64.4	35.6	42.7	53.96	9	−33
30	32	27.6	19.5	20.9	31.4	33	17.5	18.1	59.6	40.4	46.4	39.1	64.4	35.6	42.75	54.26	9	−33
31	32	27.6	19.5	20.9	31.4	33	17.5	18.1	59.6	40.4	46.5	39	64.4	35.6	42.75	54.40	9	−33
32	32	27.6	19.5	20.9	31.4	33	17.5	18.1	59.6	40.4	46.4	39	64.4	35.6	42.7	54.29	9	−33
33	32	27.6	19.5	20.9	31.3	33	17.6	18.1	59.6	40.4	46.5	39	64.3	35.7	42.75	54.26	9	−33
34	32	27.7	19.5	20.8	31.3	33.2	17.6	17.9	59.7	40.3	46.4	39.1	64.5	35.5	42.75	54.76	9	−33
35	32	27.6	19.5	20.9	31.4	33	17.5	18	59.6	40.4	46.5	39	64.4	35.6	42.75	54.24	9	−33
36	32	27.7	19.5	20.8	31.3	33.2	17.6	17.9	59.7	40.3	46.4	39.1	64.5	35.5	42.75	53.86	9	−33
37	31.7	27.7	19.7	20.9	30.8	33	18.1	18.1	59.4	40.6	46.7	38.9	63.8	36.2	42.8	54.01	9	−32
38	31.7	27.7	19.7	20.9	30.8	33	18.1	18.1	59.4	40.6	46.7	38.9	63.8	36.2	42.8	54.30	9	−32
39	31.7	27.7	19.7	20.9	30.8	33	18.1	18.1	59.4	40.6	46.7	38.9	63.8	36.2	42.8	54.20	9	−32
40	31.7	27.6	19.7	20.9	30.8	33	18.1	18.1	59.3	40.6	46.7	38.9	63.8	36.2	42.8	54.11	9	−32
41	31.7	27.7	19.7	20.9	30.8	33	18.1	18.1	59.4	40.6	46.7	38.9	63.8	36.2	42.8	54.26	9	−32
42	31.7	27.7	19.7	20.9	30.8	33	18.1	18.1	59.4	40.6	46.7	38.9	63.8	36.2	42.8	54.24	9	−32
43	31.7	27.7	19.7	20.9	30.8	33	18.1	18.1	59.4	40.6	46.7	38.9	63.8	36.2	42.8	54.20	9	−32
44	31.7	27.7	19.7	20.9	30.8	33	18.1	18.1	59.4	40.6	46.7	38.9	63.8	36.2	42.8	54.19	9	−32
45	32	27.7	19.5	20.8	31.5	33.1	17.5	18	59.7	40.3	46.4	39.1	64.6	35.4	42.75	54.21	9	−33
46	32	27.9	19.6	20.5	31.4	33.5	17.5	17.6	59.9	40.1	46.3	38.9	64.9	35.1	42.6	54.24	9	−33
47	32	27.9	19.6	20.6	31.4	33.5	17.5	17.6	59.9	40.1	46.3	38.9	64.9	35.1	42.6	54.23	9	−33
48	32	27.7	19.5	20.8	31.4	33.1	17.5	18	59.7	40.3	46.4	39	64.5	35.5	42.7	54.46	9	−33
49	32	27.7	19.5	20.8	31.4	33	17.5	18.1	59.7	40.3	46.4	39	64.4	35.6	42.7	53.63	9	−33
50	32	27.9	19.6	20.6	31.4	33.4	17.5	17.6	59.9	40.1	46.3	38.9	64.8	35.2	42.6	53.40	9	−33
51	32	27.6	19.6	20.9	31.4	32.7	17.8	18.1	59.6	40.4	46.5	38.9	64.1	35.8	42.7	54.03	9	32
52	31.9	27.5	19.6	20.9	31.2	32.6	18	18.2	59.4	40.6	46.5	39	63.8	36.2	42.75	54.09	9	−33
53	32	27.7	19.5	20.8	31.4	33.1	17.5	17.9	59.7	40.3	46.5	39.1	64.5	35.5	42.8	53.60	9	−33
54	32	27.8	19.5	20.6	31.6	33.3	17.3	17.9	59.8	40.2	46.4	39	64.9	35.1	42.7	54.46	9	−33
55	32	27.7	19.5	20.8	31.3	33.1	17.6	18	59.7	40.4	46.4	39	64.4	35.6	42.7	54.47	9	−33
56	31.9	27.5	19.6	21	31.2	32.4	18	18.4	59.4	40.6	46.6	38.8	63.6	36.3	42.7	53.53	9	−32
57	32	27.6	19.5	20.8	31.4	33.1	17.6	18	59.6	40.3	46.4	39.1	64.5	35.6	42.75	54.56	9	−33
58	32	27.6	19.5	20.9	31.4	33	17.5	18.1	59.6	40.4	46.5	39	64.4	35.6	42.75	54.09	9	−33
59	32.1	27.8	19.5	20.6	31.6	33.4	17.3	17.8	59.9	40.1	46.4	38.9	65	35.1	42.65	54.17	9	−33
60	32	27.4	19.6	21	31.4	32.4	17.9	18.4	59.4	40.6	46.6	38.9	63.8	36.2	42.75	54.44	9	−33
61	32	27.4	19.6	21	31.3	32.4	17.9	18.4	59.4	40.6	46.6	38.9	63.7	36.3	42.75	53.87	9	−33
62	31.8	27.6	19.7	20.9	30.9	32.9	18.1	18.1	59.4	40.6	46.7	38.9	63.8	36.2	42.8	54.37	9	−32
63	31.9	27.6	19.6	20.9	31.1	33	17.8	18.1	59.5	40.5	46.5	39.1	64.1	35.9	42.8	54.33	9	−33
Avg	31.9	27.7	19.6	20.8	31.3	33.0	17.7	18.0	59.6	40.4	46.5	38.9	64.3	35.7	42.7	54.20	9	−.30
SD	0.1	0.1	0.08	0.11	0.22	0.23	0.25	0.16	0.15	0.15	0.12	0.08	0.36	0.36	0.05	0.35	0	0.004

ENC effective number of codons; GRAVY general average hydropathicity; ARO aromaticity, Avg average; SD standard deviation

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