A SNP resource for Douglas-fir: de novotranscriptome assembly and SNP detection and validation

BMC Genomics

Table 6 Numbers of potential SNPs detected in Douglas-fir using an individual dataset probability value of 10 ^-4

			No. of reads (× 10⁶)	No. of unique or shared SNPs^*
Plant materials (dataset ID)	Seed source	Sequencing platform	No. of reads (× 10⁶)	Unique	Coastal	Yakima	Interior	Total^†
				--------------- All isotigs (1 isotig/isogroup (I1)) --------------
Multi-genotype #1 (MG1_SANG)	Coastal	Sanger	2.77	3982 (2606)	101,089 (85,635)	29,922 (25,523)	81,633 (69,109)	107,884 (90,487)
Multi-genotype #2 (MG2₄₅₄₎	Coastal	Roche 454
Single-genotype (SG₄₅₄)	Coastal	Roche 454
Multi-genotype #2 (MG2_IL)	Coastal	Illumina	64.00	18,694 (15,617)	192,693 (162,560)	41,952 (35,700)	146,242 (123,503)	192,693 (162,560)
Coos Bay (CB_IL)	Coastal	Illumina	13.41	1044 (895)	66,304 (56,547)	29,051 (24,703)	53,275 (45,437)	66,304 (56,547)
Yakima (YK_IL)	Yakima	Illumina	8.99	638 (545)	43,066 (36,621)	-	40,840 (34,750)	47,573 (40,505)
Interior (INT_IL)	Interior	Illumina	80.45	71,241 (61,334)	151,014 (127,403)	40,840 (34,750)	-	226,124 (192,076)
Total			169.62

^*The number of unique SNPs and the number of SNPs shared in other datasets of the coastal, Yakima, and interior seed sources are presented for all isogroups (I1 + IM) and for the 1 isotig per isogroup subset (I1) (in parentheses). The total number of unique SNPs detected in all datasets was 278,979.
^†SNP totals are not the sums of the values in the same row because SNPs are double-counted. For example, we detected 66,304 SNPs in the CB_IL dataset, 29,051 of which were detected in the YK_IL dataset and 53,275 of which were detected in the INT_IL dataset.

ISSN: 1471-2164