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

Table 3 Statistics of phasing results for the two phasing strategies

	Trusted set of variants				Traditional SNP filtering
	WGS-P1		WGS-P2		WGS-P1		WGS-P2
	Average	Median	Average	Median	Average	Median	Average	Median
Proportion of phasing errors
Per animal	50.95%	50.13%	0.38%	0.32%	50.80%	50.41%	1.10%	1.04%
Number of switches
Per animal	739.2	631.5	704.5	574	4521	4291	4387.7	4079
Per animal and chromosome	25.49	18.5	24.29	16.5	155.9	105.5	151.3	112

WGS-P1 phased with LD information only, WGS-P2 phased with both LD and familial information

ISSN: 1297-9686