An Axiom SNP genotyping array for Douglas-fir

Howe, Glenn T.; Jayawickrama, Keith; Kolpak, Scott E.; Kling, Jennifer; Trappe, Matt; Hipkins, Valerie; Ye, Terrance; Guida, Stephanie; Cronn, Richard; Cushman, Samuel A.; McEvoy, Susan

doi:10.1186/s12864-019-6383-9

BMC Genomics

Table 2 Transcript and probeset ranking variables versus genotyping success using an Axiom genotyping array

From: An Axiom SNP genotyping array for Douglas-fir

Variable	No. of probesets	Category or mean	Percent or mean		Number
Variable	No. of probesets	Category or mean	Success	Fail	Success	Fail
Transcript ranking variables^a
No. of hits to scaffolds^b (transcript mean) (v0.5)	58,350	1	58.5	41.5	18,745	13,286
		> 1	41.5	58.5	9403	13,242
		0	27.5	72.5	1011	2663
Transcript confidence score^b (absent for UH SNPs)	54,625	Higher	55.8	44.2	13,987	11,087
Transcript confidence score^b (absent for UH SNPs)	54,625	Lower	49.6	50.4	14,663	14,888
No. of SNPs per transcript^c	58,350	Mean	12.00	10.36	29,159	29,191
		Q3	56.2	43.8	9202	7173
		Q1	43.5	56.5	7375	9570
Combined rank^c (transcripts)	58,350	Mean	27,252.2	31,096.5	29,159	29,191
		Q1	52.5	47.5	7659	6930
		Q3	35.7	64.3	5214	9375
Probeset-within-transcript ranking variables
Infinium success^b,d	6173	SNP success	74.5	25.5	4598	1575
Probability of flanking SNPs^b,e	58,350	Low	50.8	49.2	27,732	26,844
Probability of flanking SNPs^b,e	58,350	Moderate	37.8	62.2	1427	2347
No. of perfect alleles^b (percent identity = 100%)(v0.5)	58,350	1	53.5	46.5	23,916	20,799
		0	39.2	60.8	5042	7810
		2	25.7	74.3	201	582
pConvert^c	57,381	Mean	0.615	0.595	28,508	28,873
		Q3	57.7	42.3	8319	6087
		Q1	41.5	58.5	6429	9059
Target SNP probability^b,f (OSU SNPs)	53,958	P < 0.0001	55.0	45.0	24,600	20,138
Target SNP probability^b,f (OSU SNPs)	53,958	P < 0.001	39.7	60.3	3658	5562
Target SNP probability^b (UH SNPs)	3725	3 programs	23.3	76.7	128	422
Target SNP probability^b (UH SNPs)	3725	2 programs	12.0	88.0	381	2794
Final rank^c,g (transcripts and probesets-within-transcripts)	58,350	Mean	27,891.8	30,457.6	29,159	29,191
		Q1	61.5	38.5	8966	5622
		Q3	46.6	53.4	6800	7788
Other variables
Recommendation^b,h	57,295	Recommended	54.7	45.3	17,779	14,748
Recommendation^b,h	57,295	Neutral	43.2	56.8	10,691	14,078

^aTranscripts refer to the Newbler isotigs [17] or putative transcripts [32] used for SNP discovery. v0.5 is version 0.5 of the Douglas-fir reference genome. UH SNPs were those detected by Müller et al. [32], whereas OSU SNPs were those detected by Howe et al. [17]
^bFor the categorical variables, percentages and numbers of probesets are reported for each category and means are absent. All differences among categories were highly significant (P < 0.0001) using a likelihood ratio chi-square test
^cFor the ranks and continuous variables, means are reported in bold, and percentages and numbers of probesets are reported for the upper (Q3) and lower (Q1) quartiles. Categories are ranked by probeset success. Successful SNPs were those that had a call rate > 60% and were polymorphic. All differences between means were highly significant (P < 0.0001) using a T-test (non-rank variables) or a Wilcoxon rank test (Combined rank and Final rank variables)
^dFor SNPs successfully genotyped with the Infinium platform, Axiom probeset success (74.5%) was significantly greater than the overall probeset success rate of 50.0% (P < 0.0001)
^eLow (rank = 1) or moderate (rank = 2) chance of having flanking SNPs or indels
^fThe P < 0.001 category indicates that 0.0001 ≤ P < 0.001
^gThe final probeset rank was based on the combined transcript rank plus the probeset-within-transcript variables
^hThe Affymetrix Recommendation variable was not used to select probesets because it is a categorical variable derived from pConvert

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ISSN: 1471-2164

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