Table 1 Effect of the selected threshold for minimal twin group size ts0 on the skeletal map length under low and moderate rates of genotyping errors and 20% of missing data points.
Map | Initial | After cleaning | After saturation | δ | |||||
---|---|---|---|---|---|---|---|---|---|
pe | Nm | ts0 | Nsk | L | Nsk | L | Nsk | L | |
0.01 | 104 | 4 | 349 | 384.2 | 81 | 172.1 | 99 | 171.8 | 1.8 |
6 | 128 | 221.0 | 65 | 173.8 | 77 | 174.9 | 2.3 | ||
8 | 108 | 237.0 | 47 | 175.5 | 65 | 174.2 | 2.7 | ||
0.02 | 3 | 237 | 397.8 | 58 | 207.3 | 71 | 187.9 | 2.7 | |
4 | 102 | 213.8 | 38 | 128.8 | 47 | 126.6 | 2.8 | ||
0.01 | 2 × 104 | 6 | 398 | 472.1 | 97 | 216.1 | 111 | 217.1 | 2.0 |
8 | 256 | 357.9 | 91 | 219.9 | 104 | 217.4 | 2.1 | ||
10 | 178 | 307.3 | 71 | 205.8 | 83 | 201.7 | 2.5 | ||
0.02 | 4 | 305 | 406.4 | 85 | 208.0 | 103 | 200.9 | 2.0 | |
5 | 175 | 333.6 | 57 | 207.6 | 73 | 194.3 | 2.7 | ||
6 | 110 | 200.6 | 42 | 135.1 | 56 | 132.5 | 2.4 | ||
0.01 | 4 × 104 | 10 | 377 | 461.7 | 140 | 244.7 | 150 | 253.2 | 1.7 |
12 | 281 | 399.4 | 110 | 244.7 | 120 | 243.5 | 2.0 | ||
16 | 195 | 339.0 | 95 | 245.0 | 108 | 248.4 | 2.3 | ||
0.02 | 6 | 289 | 446.0 | 89 | 262.4 | 115 | 249.1 | 2.2 | |
8 | 157 | 364.9 | 67 | 272.9 | 83 | 254.4 | 3.1 | ||
10 | 94 | 323.6 | 50 | 283.0 | 67 | 252.2 | 3.8 |
Simulated map length was L = 191.3, 214.6, and 273 cM for populations with Nm = 104, 2 × 104, and 4 × 104 markers, respectively; pe, level of genotyping errors per marker locus; ts, twin group size, ts0, threshold ts value: skeletal markers should obey the condition ts ≥ ts0; Nsk, number of intervals in the map; Nm, number of markers per LG in the initial dataset; δ, map density (the ratio of the entire chromosome map length to the number of intervals).