A strategy to improve phasing of whole-genome sequenced individuals through integration of familial information from dense genotype panels

Table 7 Imputation reliability (measured as r ² and given in %) for the two scenarios^a of imputation

	Trusted set of variants						Traditional variant filtering
	N	WGS-I1^a		WGS-I2^a		D ^b_I2-I1	N	WGS-I1^a		WGS-I2^a		D_I2-I1b
	N	Avg r ²	Med r ²	Avg r ²	Med r ²	D ^b_I2-I1	N	Avg r ²	Med r ²	Avg r ²	Med r ²	D_I2-I1b
Overall	5,149,267	90.47	93.63	90.65	93.81	0.18	13,129,937	88.66	93.57	89.07	93.87	0.41
NMA = 2^c	79,755	56.74	67.47	59.98	86.76	3.24	680,303	63.04	80.94	67.95	96.96	4.91
NMA = 3^c	78,933	69.10	71.02	70.78	75.35	1.68	510,080	77.28	92.25	79.00	95.49	1.72
0.01 < MAF ≤ 0.05	644,224	77.57	85.82	78.45	87.11	0.88	3,278,384	79.56	91.35	81.01	94.27	1.46
0.05 < MAF ≤ 0.10	673,955	89.15	91.65	89.21	91.81	0.06	2,047,206	89.91	92.82	90.07	93.15	0.16
0.10 < MAF	3,831,088	92.87	94.20	92.95	94.30	0.08	7,804,347	92.15	93.91	92.19	93.96	0.04
First Mb	48,089	85.40	90.90	87.56	92.84	2.15	134,266	83.17	90.10	85.19	92.27	2.01
Last Mb	53,502	87.94	91.55	88.45	92.05	0.51	155,246	85.85	91.26	86.53	91.88	0.68
Between first and last Mb	5,045,959	90.55	93.68	90.70	93.84	0.16	12,840,425	88.75	93.62	89.14	93.91	0.39

^aWGS-I1: imputation from GEN-P1 to WGS-P1 (using only LD information); WGS-I2: imputation from GEN-P2 to WGS-P2 (using both LD and familial information)
^bD_I2-I1: difference of average r ²
^cNMA: number of occurrences of the minor allele

ISSN: 1297-9686