Table 2 Comparison of linkage mapping results using assembled genome, gene models, and repeat masked genome as reference for scoring RADseq markers
Unmasked genome as reference | Gene models as reference | Repeat Masked genome as reference | |||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Linkage group (number of markers) | Linkage group (number of markers) | Linkage group (number of markers) | |||||||||||||||||||||||||||||
Scaffolds | LG | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
1 | 1 | 818 | 18 | 30 | 489 | 13 | 109 | 14 | 26 | 8 | 14 | 79 | 0 | 0 | 0 | 45 | 2 | 0 | 3 | 0 | 0 | 2 | 859 | 1 | 0 | 3 | 0 | 0 | 3 | 0 | 2 |
2 | 3 | 21 | 17 | 17 | 35 | 12 | 592 | 15 | 15 | 4 | 5 | 2 | 7 | 75 | 0 | 1 | 2 | 0 | 2 | 0 | 0 | 0 | 6 | 8 | 433 | 0 | 0 | 0 | 5 | 0 | 1 |
3 | 2 | 5 | 743 | 7 | 19 | 2 | 29 | 0 | 3 | 8 | 17 | 2 | 90 | 0 | 3 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 4 | 669 | 0 | 0 | 0 | 4 | 0 | 0 | 0 |
4 | Â | 2 | 2 | 0 | 14 | 0 | 12 | 0 | 3 | 5 | 2 | 0 | 5 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 4 | 3 | 3 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
5 | 8 | 8 | 7 | 1 | 27 | 8 | 40 | 9 | 3 | 195 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 31 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | 205 | 0 |
6 | 5 | 0 | 3 | 1 | 17 | 386 | 17 | 2 | 0 | 1 | 0 | 0 | 0 | 1 | 65 | 0 | 7 | 0 | 0 | 0 | 0 | 2 | 1 | 1 | 2 | 0 | 430 | 0 | 0 | 0 | 0 |
7 | 4 | 6 | 2 | 543 | 21 | 1 | 30 | 1 | 3 | 2 | 10 | 2 | 0 | 2 | 1 | 0 | 55 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 335 | 0 | 0 | 0 | 0 | 0 |
8 | 6 | 6 | 5 | 8 | 17 | 0 | 32 | 8 | 297 | 12 | 7 | 0 | 1 | 0 | 0 | 0 | 0 | 34 | 0 | 1 | 0 | 0 | 5 | 3 | 1 | 0 | 0 | 222 | 0 | 0 | 1 |
9 | 7 | 0 | 2 | 0 | 3 | 0 | 11 | 289 | 3 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 29 | 0 | 0 | 0 | 1 | 0 | 2 | 1 | 0 | 0 | 225 | 0 | 0 |
10 | 9 | 15 | 7 | 7 | 21 | 1 | 20 | 0 | 0 | 2 | 268 | 1 | 0 | 0 | 3 | 1 | 0 | 2 | 0 | 0 | 11 | 2 | 1 | 0 | 0 | 0 | 2 | 0 | 1 | 0 | 156 |