An Axiom SNP genotyping array for Douglas-fir

BMC Genomics

Table 4 SNP ranking variables versus SNP genotyping success using an Axiom genotyping array

Variable^a	No. of SNPs	Category	Percent		Number
Variable^a	No. of SNPs	Category	Success	Fail	Success	Fail
Percent identity (PID)^b,c
Scaffold PID (best hit)	55,766	> 80	50.9	49.1	27,936	26,906
Scaffold PID (best hit)	55,766	≤ 80	17.1	82.9	158	766
Scaffold PID (second-best hit)	55,766	≤ 80	59.9	40.1	22,775	15,218
Scaffold PID (second-best hit)	55,766	> 80	29.9	70.1	5319	12,454
Scaffold PID (best-hit, second-best hit)	55,766	> 80, ≤ 80	61.0	39.0	22,617	14,452
		> 80, > 80	29.9	70.1	5319	12,454
		≤ 80, ≤ 80	17.1	82.9	158	766
Number of hits^b
Number of hits to scaffolds	55,766	1	60.9	39.1	22,946	14,753
		> 1	29.1	70.9	4980	12,115
		0	17.3	82.7	168	804
Number of hits to singletons	55,766	0	51.5	48.5	27,922	26,319
		1	11.8	88.2	79	589
		> 1	10.9	89.1	93	764
Number of hits to gene models	55,766	1	55.8	44.2	10,760	8522
		0	50.8	49.2	16,208	15,705
		> 1	24.6	75.4	1126	3445
Number of hits to reference transcripts	55,766	1	54.1	45.9	12,389	10,529
		> 1	47.9	52.1	3618	3943
		0	47.8	52.2	12,087	13,200

^aSNP variables are the numbers of BLAST hits or percent identities (PID) using v1.0 of the Douglas-fir reference genome (scaffolds, singletons, gene models, or transcripts) as the target and SNP sequences (71-mers) as the queries. Percentages and numbers of SNPs are reported for each category. Successful SNPs were those that had a call rate > 60% and were polymorphic
^bAll differences among categories were highly significant (P < 0.0001) using a likelihood ratio chi-square test
^cSNP blast hits were categorized as either > 80% or ≤ 80% identity (PID)

ISSN: 1471-2164