Table 1.

Effect of the Depth of Sequence Alignment, the VarScan P Value, and the MAF upon the Number of Predicted SNPs and the True Positive Rate in P. glauca

	Number of Nonsingleton SNPs with a MAF ≥1%	Number of Nonsingleton SNPs Tested by Infinium iSelect Genotypinga	Number of Nonsingleton SNPs Successfully Genotyped	Minimum TP rate (%)b
Depth of sequence alignment
0–10	24,115	155	117	75.5
10–20	40,340	332	283	85.2
20–30	33,934	307	262	85.3
30–40	28,496	288	250	86.8
40–50	24,563	292	246	84.2
50–100	83,399	1,154	1,018	88.2
100–150	50,356	862	746	86.5
150–200	35,992	602	503	83.5
≥200	52,491	1,946	1,784	91.7
Total	373,686	5,938	5,209	87.7
SNP P value computed by VarScanc
0.00–0.05	193,437	4,789	4,420	92.3
0.05–0.10	21,616	174	150	86.2
0.10–0.15	39,025	277	212	76.5
0.15–0.20	0	0	0	—
0.20–0.25	95,493	543	310	57.1
≥0.25	0	0	0	—
Total	349,571	5,783	5,092	88.1
MAFd
0.01–0.05	33,176	404	356	88.1
0.05–0.10	37,859	586	532	90.8
0.10–0.15	29,481	596	548	91.9
0.15–0.20	22,667	477	442	92.7
0.20–0.25	19,281	544	508	93.4
0.25–0.30	17,615	489	453	92.6
0.30–0.35	15,052	481	433	90.0
0.35–0.40	13,270	472	435	92.2
0.40–0.45	13,665	470	439	93.4
0.45–0.50	12,987	444	424	95.5
Total	215,053	4,963	4,570	92.1

Note.—The true positive rate was determined from 5,938 genotyped SNPs.

^aSNPs predicted by VarScan and genotyped with the PgAS1 Infinium SNP array (Pavy et al. 2013).

^bThis is a minimum rate, given that the success rate of the Infinium iSelect high-throughput genotyping array PgAS1 reached 92.3% for P. glauca SNPs previously confirmed by other means (see Pavy et al. 2013).

^cSubset of SNPs predicted with a depth of alignment ≥10.

^dSubset of SNPs predicted with a depth of alignment ≥10 and a VarScan P < 0.10.