Inversion symmetry of DNA k-mer counts: validity and deviations

Shporer, Sagi; Chor, Benny; Rosset, Saharon; Horn, David

doi:10.1186/s12864-016-3012-8

BMC Genomics

Table 4 Evaluation of E[|Z|], E[X], fraction of unrealized inverse pairs, and chromosomal length

From: Inversion symmetry of DNA k-mer counts: validity and deviations

	k	HG38	HG38M	HG18	HG18M	Mouse	MouseM	C eleg	Cerevisiae	Ecoli
E[\|Z\|]	1	4.154	3.943	4.560	5.406	6.928	11.001	2.814	2.057	1.273
	2	2.581	2.316	3.260	3.417	3.695	5.652	1.548	1.682	1.479
	3	1.707	1.769	1.983	2.152	2.780	3.904	1.589	1.434	1.318
	4	1.446	1.392	1.339	1.492	1.809	2.342	1.397	1.000	1.012
	5	1.202	1.186	1.069	1.133	1.262	1.490	1.216	0.867	0.921
	6	1.057	1.001	0.930	0.943	0.990	1.070	1.075	0.791	0.852
	7	0.984	0.935	0.894	0.884	0.892	0.902	0.980	0.780	0.837
	8	0.929	0.883	0.867	0.845	0.843	0.839	0.893	0.787	0.815
	9	0.881	0.855	0.843	0.828	0.823	0.819	0.851	0.841	0.811
	10	0.844	0.831	0.825	0.816	0.815	0.813	0.824	0.902	0.815
	11	0.825	0.821	0.816	0.814	0.813	0.814	0.835	0.940	0.856
	12	0.824	0.829	0.821	0.826	0.822	0.828	0.881	0.956	0.916
E[X]	1	0.00038	0.00050	0.00041	0.00067	0.00068	0.00152	0.00099	0.00672	0.00083
	2	0.00046	0.00058	0.00058	0.00083	0.00070	0.00150	0.00111	0.01021	0.00196
	3	0.00067	0.00095	0.00077	0.00106	0.00121	0.00218	0.00260	0.01752	0.00350
	4	0.00134	0.00179	0.00115	0.00170	0.00165	0.00283	0.00474	0.02527	0.00554
	5	0.00247	0.00329	0.00206	0.00284	0.00260	0.00397	0.00839	0.04547	0.01067
	6	0.00470	0.00593	0.00402	0.00537	0.00461	0.00636	0.01535	0.08576	0.02075
	7	0.00942	0.01205	0.00852	0.01123	0.00941	0.01222	0.02905	0.18223	0.04362
	8	0.01918	0.02472	0.01809	0.02355	0.01954	0.02505	0.05593	0.38663	0.08975
	9	0.03951	0.05169	0.03850	0.04998	0.04226	0.05334	0.11437	0.64905	0.18551
	10	0.08380	0.10979	0.08334	0.10736	0.09343	0.11601	0.24551	0.82906	0.36850
	11	0.17518	0.22274	0.17538	0.21909	0.19196	0.23044	0.47655	0.91443	0.61571
	12	0.31969	0.38249	0.32051	0.37838	0.33829	0.38843	0.68957	0.94564	0.81471
Fraction of null pairs	7								0.00110
	8								0.04863	0.00079
	9		0.00001		0.00001		0.00002		0.48397	0.00954
	10	0.00042	0.00130	0.00042	0.00127	0.00101	0.00217	0.00552	2.39166	0.06538
	11	0.01460	0.02590	0.01471	0.02515	0.02289	0.03312	0.14178	9.83436	0.30279
	12	0.09259	0.14336	0.09292	0.13934	0.11537	0.15551	0.85693	39.18	0.66052
length		2.3E + 08	1.1E + 08	2.2E + 08	1.2E + 08	1.9E + 08	1.1E + 08	1.5E + 07	230218	4639664

Displayed results are for chr1 of HG38, HG18, mouse, C elegans, and S cerevisiae, and for the full bacterial chromosome of E coli. M refers to masked chromomes. Centromere regions were removed from the HG 38 data. Highlighted results are the ones determining the k-limit, KL, of the different chromosomes

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