Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce

Table 3 Missing data. Rate of missing data per valid segregating SNP according to classes of GenTrain scores for each of white spruce and black spruce.

Species	Class of GenTrain scores	Number of SNPs assayed	Number of segregating SNPs	Number of monomorphic SNPs	Average number of missing data per SNP scored	Average call rate per SNP scored (%)¹
White spruce
	<0.25	165	0	0	-	-
	0.25–0.3	0	0	0	-	-
	0.3–0.4	3	3	0	11.0	96.2
	0.4–0.5	15	10	5	2.2	99.2
	0.5–0.6	46	33	13	1.9	99.3
	0.6–0.7	92	81	11	1.4	99.5
	0.7–0.8	323	302	21	1.6	99.4
	0.8–0.9	118	82	36	2.4	99.1
	>0.90	6	5	1	2.8	100
	Total	768	516	87	-	-
	Weighted average	-	-	-	1.8	99.4
Black spruce
	<0.25	138	0	0	-	-
	0.25–0.3	0	0	0	-	-
	0.3–0.4	10	10	0	3.5	98.8
	0.4–0.5	17	16	1	4.5	98.4
	0.5–0.6	80	74	6	1.9	99.3
	0.6–0.7	79	72	6	2.3	99.3
	0.7–0.8	170	163	7	0.7	99.8
	0.8–0.9	260	244	16	0.5	99.8
	>0.90	14	13	1	2.0	99.3
	Total	768	592	31	-	-
	Weighted average	-	-	-	1.1	99.6

ISSN: 1471-2164