. 2017 May 16;206(3):1285–1295. doi: 10.1534/genetics.116.197491

Table 3. The effect of population size (n) on map characteristics.

ms%	p_e	ts₀	r	L_t1	N_t1sk	δ_t1	L_c	N_csk	δ_c	L_t2	N_t2sk	δ_t2	L	N_sk	δ	n_e	n_r	m_c%	l_f%
Nm = 10⁴, n = 200
0	0			67	41	1.6	41	64	0.6	82	39	2.1	191	144	1.3	0	0	100	0
20	0.01	6		58	18	3.2	39	40	1.0	78	18	4.3	175	76	2.3	3	7	99.5	52
Nm = 10⁴, n = 500
0	0			84	47	1.8	37	118	0.3	85	52	1.6	206	217	0.9	0	0	100	0
20	0.01	3	0.01	94	33	2.8	38	42	0.9	89	28	3.2	238	103	2.3	1	10	100	57
Nm = 10⁴, n = 10³
0	0			73	55	1.3	40	194	0.2	85	65	1.3	198	314	0.6	0	0	100	0
20	0.01	2	0.01	86	27	3.2	85	66	1.3	107	38	2.8	278	131	2.1	2	12	100	62

p_e, level of genotyping errors per marker; ms, simulated rate of missing data per marker; N_m, number of markers per LG in the initial dataset; ts, twin group size, ts₀, threshold ts value: skeletal markers should obey the condition ts ≥ ts₀; r, kernel radius; L, L_t1, L_t2, and L_c, the estimated genetic lengths (in centimorgans) of the entire chromosome map and its subtelomeric and near-centromeric regions, while N_sk, N_t1sk, N_t2sk, and N_csk are the corresponding numbers of intervals of the entire map and its subtelomeric and peri-centromeric regions; δ, δ_t1,δ_t2, and δ_c, map density (centimorgan/interval) of the entire map and its subtelomeric and peri-centromeric regions; n_e, the number of errors in the estimated order of markers compared to the simulated order; n_r, the number of “repeats” caused by fission of the initial TGs into subgroups due to genotyping errors and missing marker scores; m_c (%), map coverage, which represents the proportion of the constructed skeletal map length relative to the simulated map length; l_f (%), loss factor, the percentage of lost (noncharacterized) map unique positions in the constructed skeletal map compared to the simulated map; it is calculated as l_f = 100 [N_skef − (N_sk − n_r)]/N_skef, = 100 (N_skef − N_sk + n_r)/N_skef, where N_skef represents the number of intervals in the skeletal maps built for the simulated error-free data, while N_sk and (N_sk − n_r) represent the number of noisy markers in the skeletal map, noncorrected and corrected for the number of repeats, respectively.