Patterns of nucleotides that flank substitutions in human orthologous genes

BMC Genomics

Table 1 Parameters estimated by Equation 2 for substitutions occurring at the third-codon positions.

Category	Native^A				Codon shuffling^{B, D}				Synonymous codon shuffling^{C, D}
	R²	Peak Loc .	A	ω	R²	Peak Loc .	A	ω	R²	Peak Loc .	A	ω
All	0.863	3n - 0.275	0.007	2.997	0.994	3n - 0.205	0.005	2.997	0.983	3n - 1.218	0.014	3.001
TS	0.844	3n - 0.312	0.007	2.998	0.997	3n - 0.255	0.006	2.998	0.979	3n - 1.203	0.015	3.000
TV	0.438	3n - 0.062	0.005	2.995	0.947	3n + 0.043	0.004	2.996	0.917	3n - 1.293	0.012	3.001
C→T	0.930	3n - 0.006	0.029	2.999	0.999	3n + 0.017	0.027	3.000	0.916	3n - 1.275	0.012	3.001
A→G	0.852	3n - 1.156	0.015	3.000	0.999	3n - 1.151	0.015	3.000	0.929	3n - 1.137	0.018	3.000
G→A	0.833	3n - 0.088	0.014	3.001	0.995	3n - 0.065	0.007	2.998	0.924	3n - 1.239	0.015	3.000
T→C	0.787	3n - 1.068	0.011	3.000	0.998	3n - 1.032	0.009	3.000	0.940	3n - 1.141	0.017	3.000
G→T	0.724	3n + 0.059	0.031	3.000	0.998	3n + 0.067	0.027	3.000	0.547	3n - 1.383	0.011	2.997
C→A	0.721	3n + 0.061	0.026	2.997	0.914	3n - 1.925	0.019	3.000	0.487	3n - 1.397	0.010	3.009
C→G	0.703	3n + 0.051	0.025	3.002	0.997	3n + 0.040	0.026	3.000	0.561	3n - 1.377	0.009	2.996
G→C	0.644	3n + 0.195	0.027	2.999	0.993	3n + 0.202	0.028	3.000	0.594	3n - 1.628	0.014	3.002
T→G	0.495	3n - 1.182	0.015	3.001	0.996	3n - 1.181	0.015	3.000	0.667	3n - 1.141	0.018	3.002
A→C	0.482	3n - 1.198	0.016	3.001	0.996	3n - 1.187	0.016	3.001	0.669	3n - 1.138	0.021	3.001
T→A	0.342	3n - 1.128	0.014	3.001	0.997	3n - 1.210	0.015	3.001	0.546	3n - 1.123	0.019	3.001
A→T	0.321	3n - 1.062	0.017	3.000	0.973	3n - 1.044	0.015	3.002	0.591	3n - 1.133	0.025	3.000

A: Parameters for fitting the periodic signals in the native flanking sequences, given that the region between site ±2 was excluded. B: Parameters for fitting the periodic signals in the corresponding codon-shuffled sequences. C: Parameters for fitting the periodic signals in the corresponding synonymous-codon-shuffled sequences, given that the region between site ±2 was excluded. D: Parameters were estimated from the mean for 1,000 independent random datasets. The following abbreviations and symbols are used in the table: Peak Loc represents peak location in the periodicity; A denotes amplitude; 3n means the multiple of three, corresponding to the third-codon positions; ω denotes how many nucleotide sites occur in an interval; All represents all substitutions; TS and TV represent transition and transversion, respectively.

ISSN: 1471-2164