Table 3.

Summary of LD and SNPs used to estimate LD.

Chromosome	No. of SNPs	Density of SNPs (No. of SNPs/10 kb)	No. of SNPs used to estimate LD1	Mean r2	LD extent (kb)
Ca1	20,837	4.25	2,979	0.06	400
Ca2	11,181	3.01	2,826	0.03	200
Ca3	19,487	2.92	1,674	0.15	4,000
Ca4	25,323	4.30	7,106	0.02	200
Ca5	18,313	2.64	1,428	0.07	200
Ca6	15,620	2.37	2,469	0.05	150
Ca7	13,272	2.36	2,070	0.03	200
Ca8	4,740	2.38	933	0.06	200
Unassembled contigs	16,004	3.25	NA	NA	NA
Total/average	144,777		21,485	0.06	700

¹SNPs with high confidence (minimum five reads per genotype).