An Axiom SNP genotyping array for Douglas-fir

BMC Genomics

Table 1 Percentages of successful SNPs using an Axiom genotyping array in Douglas-fir

SNP category^b	Final SNP call rate threshold^a					Affymetrix abbreviation [11]
	Default	Rescue
	97%	90%	80%	70%	60%
Off-target variant	1	1	1	1	1	OTV
Other	30	29	26	24	23	Other
Call rate below threshold	8	3	2	2	2	CallRateBelowThreshold
Not Converted	40	34	30	27	26	OTV + Other + CallRateBelowThreshold
No minor homozygote	13	13	13	13	13	NoMinorHom
Monomorphic high resolution	16	16	16	16	16	MonoHighResolution
Polymorphic high resolution	31	31	31	31	31	PolyHighResolution
Rescued	–	6	10	13	13	Rescued from Other and CallRateBelowThreshold
Converted^c	60	66	70	73	74	PolyHighResolution + NoMinorHom + MonoHighResolution + Rescued
Percent successful (population ave)	31.5	37.5	41.6	44.0	44.9	PolyHighResolution + Rescued
Number successful (population ave)	17,555	20,926	23,223	24,548	25,037	PolyHighResolution + Rescued
Percent successful (population sum)	37.1	42.9	46.9	49.5	50.4	PolyHighResolution + Rescued
Number successful (population sum)	20,669	23,917	26,180	27,616	28,094	PolyHighResolution + Rescued

^aWe applied QC thresholds in one or two phases of analysis. The Default protocol consisted of the default Affymetrix parameters, including a CR threshold of 97%. In the Rescue protocols, we used the Default thresholds for phase 1, but then applied lower CR thresholds (60–90%) to the Other and CallRateBelowThreshold categories in phase 2
^bSNPs (N = 55,766) were classified into six categories (OTV, Other, CallRateBelowThreshold, NoMinorHom, MonoHighResolution, PolyHighResolution) and one Rescued category. Successful SNPs were those that were polymorphic with a call rate (CR) exceeding the indicated CR threshold after one or two phases of analysis with alternative quality control (QC) thresholds. Table values are averages from two populations (C1/I1 and C2) that were analyzed separately, except for the ‘population sum’ rows, which are based on sums. The C1/I1 population consisted of coastal Douglas-fir (N = 1682) and interior Douglas-fir (N = 12) samples that passed QC thresholds and were analyzed together. The C2 population consisted of coastal Douglas-fir (N = 348) samples that passed QC thresholds and were analyzed independently
^cConverted SNPs were those that were successfully assayed using the Default or Rescue protocol, but not necessarily polymorphic

ISSN: 1471-2164