Analysis of Synonymous Codon Usage Bias in Flaviviridae Virus

Table 1

The basic information of Flaviviridae.

Organism/Name	Accession id	ENC		GC12	GC3	Gravy	Aromo	CAI
Aedes flavivirus	NC_012932.1	58.97	0.502	0.501	0.5241	-0.057	0.080	0.682
Alkhurma hemorrhagic fever virus	NC_004355.1	56.85	0.451	0.553	0.4625	-0.797	0.062	0.715
Apoi virus	NC_003676.1	54.49	0.411	0.497	0.4193	-0.751	0.075	0.713
Bagaza virus	NC_012534.1	54.46	0.429	0.508	0.5207	-1.006	0.065	0.73
Banzi virus	NC_029054.1	52.79	0.518	0.504	0.4394	-0.112	0.082	0.74
Bouboui virus	NC_033693.1	54.42	0.423	0.495	0.5486	-0.882	0.073	0.722
Bussuquara virus	NC_009026.2	54.19	0.491	0.499	0.4367	-0.151	0.082	0.712
Cell fusing agent virus	NC_001564.2	57.10	0.426	0.522	0.4365	-0.599	0.078	0.683
Chaoyang virus	NC_017086.1	56.19	0.437	0.495	0.4515	-0.894	0.076	0.724
Culex flavivirus	NC_008604.2	54.87	0.582	0.529	0.6034	-0.019	0.095	0.702
Dengue virus 1	NC_001477.1	52.15	0.424	0.476	0.4314	-1.016	0.065	0.742
Dengue virus 2	NC_001474.2	48.85	0.421	0.457	0.4587	-0.226	0.077	0.701
Dengue virus 3	NC_001475.2	49.43	0.432	0.464	0.468	-0.219	0.078	0.696
Dengue virus 4	NC_002640.1	50.90	0.445	0.470	0.4808	-0.188	0.081	0.703
Donggang virus	NC_016997.1	57.18	0.440	0.501	0.4526	-0.756	0.097	0.714
Edge Hill virus	NC_030289.1	53.61	0.416	0.491	0.4311	-0.806	0.088	0.728
Entebbe bat virus	NC_008718.1	55.04	0.411	0.516	0.4254	-0.905	0.060	0.71
Gadgets Gully virus	NC_033723.1	55.54	0.443	0.532	0.4574	-0.872	0.068	0.735
Hanko virus	NC_030401.1	55.43	0.456	0.465	0.4866	-0.021	0.100	0.675
Ilheus virus	NC_009028.2	56.12	0.447	0.535	0.4595	-0.968	0.060	0.715
Japanese encephalitis virus	NC_001437.1	55.49	0.524	0.516	0.5523	-0.209	0.081	0.72
Jugra virus	NC_033699.1	53.93	0.421	0.493	0.4343	-0.873	0.069	0.718
Kadam virus	NC_033724.1	56.45	0.449	0.539	0.4596	-0.851	0.066	0.729
Kamiti River virus	NC_005064.1	56.76	0.407	0.511	0.423	-0.666	0.081	0.681
Karshi virus	NC_006947.1	56.10	0.444	0.555	0.4546	-0.804	0.064	0.717
Kedougou virus	NC_012533.1	53.46	0.583	0.544	0.6084	-0.125	0.081	0.74
Kokobera virus	NC_009029.2	53.67	0.498	0.496	0.5271	-0.161	0.083	0.711
Langat virus	NC_003690.1	55.94	0.454	0.555	0.4622	-0.803	0.054	0.723
Louping ill virus	NC_001809.1	53.88	0.580	0.548	0.6059	-0.150	0.080	0.736
Meaban virus	NC_033721.1	56.71	0.448	0.556	0.4639	-0.894	0.069	0.721
Mercadeo virus	NC_027819.1	56.50	0.549	0.506	0.5734	-0.059	0.101	0.699
Modoc virus	NC_003635.1	51.61	0.391	0.467	0.4469	-0.701	0.092	0.727
Montana myotis leukoencephalitis virus	NC_004119.1	49.63	0.372	0.439	0.4083	-0.127	0.090	0.694
Mosquito flavivirus	NC_021069.1	56.52	0.412	0.534	0.4148	-0.667	0.066	0.673
Murray Valley encephalitis virus	NC_000943.1	54.42	0.434	0.498	0.4245	-0.925	0.086	0.734
New Mapoon virus	NC_032088.1	56.42	0.445	0.530	0.4431	-0.983	0.067	0.714
Nounane virus	NC_033715.1	54.51	0.496	0.497	0.5306	-0.138	0.088	0.71
Ntaya virus	NC_018705.3	53.72	0.427	0.493	0.4402	-0.904	0.070	0.728
Ochlerotatus caspius flavivirus	NC_034242.1	56.55	0.405	0.483	0.4159	-0.612	0.092	0.696
Omsk hemorrhagic fever virus	NC_005062.1	56.13	0.443	0.545	0.4534	-0.888	0.061	0.72
Palm Creek virus	NC_033694.1	54.98	0.498	0.495	0.5267	0.008	0.095	0.682
Paraiso Escondido virus	NC_027999.1	54.68	0.423	0.487	0.4398	-0.804	0.082	0.723
Parramatta River virus	NC_027817.1	56.73	0.409	0.485	0.4202	-0.646	0.093	0.693
Phnom Penh bat virus	NC_034007.1	52.49	0.405	0.461	0.4168	-0.638	0.106	0.72
Powassan virus	NC_003687.1	55.72	0.442	0.545	0.4515	-0.799	0.061	0.718
Quang Binh virus	NC_012671.1	56.38	0.564	0.523	0.4369	-0.008	0.094	0.698
Rio Bravo virus	NC_003675.1	50.00	0.364	0.432	0.4070	-0.117	0.095	0.689
Saboya virus	NC_033697.1	54.45	0.426	0.492	0.4370	-0.832	0.077	0.724
Saumarez Reef virus	NC_033726.1	56.15	0.450	0.548	0.4641	-0.919	0.071	0.728
Sepik virus	NC_008719.1	54.34	0.412	0.483	0.4262	-0.811	0.083	0.717
Spanish goat encephalitis virus	NC_027709.1	55.92	0.449	0.559	0.4575	-0.862	0.060	0.724
Spondweni virus	NC_029055.1	56.95	0.444	0.532	0.4526	-0.938	0.058	0.715
St. Louis encephalitis virus	NC_007580.2	53.85	0.428	0.507	0.4395	-0.988	0.067	0.727
Tamana bat virus	NC_003996.1	48.75	0.345	0.402	0.3560	-0.674	0.126	0.704
Tembusu virus	NC_015843.2	54.69	0.434	0.503	0.4469	-0.894	0.078	0.727
Tick-borne encephalitis virus	NC_001672.1	55.79	0.448	0.552	0.4560	-0.777	0.064	0.722
Uganda S virus	NC_033698.1	52.78	0.430	0.469	0.4643	-0.111	0.085	0.701
Usutu virus	NC_006551.1	55.13	0.516	0.511	0.5428	-0.165	0.083	0.721
Wesselsbron virus	NC_012735.1	54.89	0.415	0.487	0.4303	-0.801	0.086	0.717
West Nile virus 1	NC_009942.1	56.15	0.438	0.522	0.5509	-0.973	0.061	0.714
West Nile virus 2	NC_001563.2	54.62	0.522	0.510	0.4432	-0.150	0.083	0.729
Yaounde virus	NC_034018.1	52.50	0.514	0.505	0.5447	-0.160	0.083	0.721
Yellow fever virus	NC_002031.1	54.54	0.413	0.509	0.4257	-0.822	0.084	0.731
Yokose virus	NC_005039.1	54.33	0.403	0.483	0.4151	-0.875	0.073	0.718
Zika virus	NC_012532.1	54.21	0.439	0.520	0.4495	-0.904	0.063	0.728