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		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

LG: linkage group.