Grouping of genomic markers in populations with family structure

BMC Bioinformatics

Table 1 Number of groups, number of groups with at least three SNPs and Calinski–Harabasz index (CH)

	Families	QTLs	Family approach				Population-LD approach
	Families	QTLs	SNPs	Groups	≥ 3	CH	SNPs	Groups	≥ 3	CH
Simulation	10	2	283	59	10	80.7	300	21	9	40.0
	10	5	282	61	10	75.0	300	17	9	38.9
	5	2	282	61	10	71.9	300	29	8	32.6
	5	5	281	64	10	85.6	300	24	9	35.0
	1	2	281	59	9	61.4	300	56	6	20.5
	1	5	282	59	9	83.0	300	49	7	25.0
Mouse	138		394	83	49	38.8	394	98	51	20.6
Cattle	5		237	172	11	2.9	300	210	11	2.4
Maize	13		953	426	93	10.4	956	576	70	21.9

Number of SNPs corresponds to the method applied (family or population LD). Average values of 100 repetitions are presented for simulated data and \(t=0.8\). Computing time for grouping markers was up to 0.2 s except for the maize data which required 2 s

ISSN: 1471-2105