An Axiom SNP genotyping array for Douglas-fir

BMC Genomics

Table 3 SNP ranking variables versus genotyping success using an Axiom genotyping array and stepwise logistic regression

Variable	DF	Array design variables (ROC area = 0.6449)^a			Final selected variables (ROC area = 0.6781)^a
Variable	DF	Step entered	Chi-square statistic	Chi-square probability	Step entered	Chi-square statistic	Chi-square probability
Scaffold PID (best-hit – second-best hit) (v1.0)^b	1	–	–	–	1	4557.23	< 0.0001
No. of hits to scaffolds (transcript mean) (v0.5)^c,d	2	1	1531.38	< 0.0001	–	–	–
Target SNP probability	1	3	642.62	< 0.0001	2	588.16	< 0.0001
pConvert	1	2	730.04	< 0.0001	3	291.26	< 0.0001
Number of perfect alleles (PID = 100%) (v0.5)^c	2	4	302.18	< 0.0001	–	–	–
Number of SNPs per transcript^d	66	5	285.60	< 0.0001	–	–	–
Number of hits to singletons (v1.0)^b	2	–	–	–	4	141.07	< 0.0001
Number of hits to gene models (v1.0)^b	2	–	–	–	5	85.06	< 0.0001
Number of hits to scaffolds (v1.0)^b	2	–	–	–	6	31.73	< 0.0001
Probability of flanking SNPs	1	6	43.55	< 0.0001	7	20.08	< 0.0001
Scaffold second-best hit PID (v1.0)^b	1	–	–	–	8	21.18	< 0.0001
Transcript confidence score	1	7	6.77	0.0093	9	12.91	0.0003
No. of hits to reference transcripts (v1.0)^b	2	–	–	–	10	14.67	0.0007

^aArray design variables included variables calculated using v0.5 of the Douglas-fir reference genome. After genotyping, alternative variables were calculated using v1.0 of the reference genome and included in the set of final selected variables. Successful SNPs were those that had a call rate > 60% and were polymorphic. ROC area is the area under the receiver operating characteristic curve using cross-validation
^bv1.0 variables are the number 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
^cv0.5 variables were calculated using BLAST, Douglas-fir reference scaffolds (v0.5) as the target, and SNP sequences (71-mers) as the queries
^dExcept for ‘reference transcripts,’ ‘transcript’ refers to the Newbler isotigs used for SNP discovery by Howe et al. [17]

ISSN: 1471-2164