Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

Table 2 Summary of the key individuals for re-sequencing

Animal ID	Clean Reads	Mapped reads rate	Depth of coverage	Uniquely mapped reads rate	SC	GC	NRS	NRD
1	90,735,760	0.951	15.81	0.942	0.988	0.979	0.972	0.042
2	117,996,876	0.964	12.87	0.959	0.998	0.928	0.947	0.128
3	105,660,610	0.938	16.21	0.928	0.975	0.979	0.961	0.040
4	125,426,182	0.953	17.11	0.947	0.974	0.976	0.954	0.047
5	111,564,528	0.956	13.60	0.951	0.997	0.985	0.989	0.029
6	127,019,556	0.960	14.68	0.955	0.998	0.957	0.968	0.079
7	99,058,934	0.873	15.11	0.864	0.990	0.976	0.974	0.046
8	130,604,192	0.961	15.19	0.956	0.953	0.991	0.951	0.018
9	141,700,352	0.961	16.25	0.956	0.999	0.991	0.995	0.017
10	141,847,268	0.965	14.39	0.960	0.999	0.991	0.995	0.018
11	115,053,394	0.958	13.92	0.953	0.997	0.986	0.989	0.026
12	141,220,480	0.965	14.41	0.961	0.999	0.992	0.995	0.016
13	126,408,732	0.959	14.44	0.951	0.997	0.953	0.964	0.087
14	137,853,286	0.963	14.79	0.958	0.998	0.989	0.993	0.022
15	124,123,884	0.961	13.92	0.955	0.998	0.987	0.991	0.026
16	134,906,464	0.970	13.88	0.965	0.999	0.990	0.995	0.020
17	137,609,612	0.957	13.77	0.950	0.998	0.988	0.992	0.024
18	140,592,166	0.954	14.53	0.946	0.998	0.990	0.993	0.020
19	120,575,426	0.955	14.53	0.949	0.996	0.986	0.988	0.028
20	131,305,824	0.962	14.29	0.957	0.998	0.980	0.988	0.038
21	140,828,990	0.964	15.43	0.959	0.997	0.989	0.992	0.020
22	134,838,280	0.965	14.33	0.960	0.998	0.966	0.977	0.064
23	115,132,512	0.951	13.51	0.944	0.997	0.988	0.989	0.024
24	112,104,986	0.953	13.84	0.947	0.998	0.989	0.990	0.022

SC SNP concordance, GC Genotype concordance, NRS Non-reference sensitivity, NRD Non-reference discrepancy

ISSN: 2049-1891