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

BMC Genomics

Table 1 Sequence datasets used to construct the Douglas-fir reference transcriptome*

Plant materials (dataset ID) *Collection information*	Method^†*cDNA library*	Total reads in dataset (%)	Number of reads filtered from the input dataset (% of library total)
			Short or low-quality	Adapter or vector	Chloro-plast	Mitochon-drial	rRNA	Retro-transposon
Multi-genotype #1 (MG1_SANG)	Sanger	12,157 (100)	57 (0.47)	0 (0.00)	2 (0.02)	2 (0.02)	0 (0.00)	1 (0.01)
Cold season	Normalized
Greenhouse	Non-normalized
Multi-genotype #2 (MG2₄₅₄)	GS-FLX Titanium	1,709,211 (100)	6649 (0.39)	1893 (0.11)	8570 (0.50)	5519 (0.32)	7264 (0.42)	11,114 (0.65)
Cold and warm seasons	Normalized	1,709,211 (100)	6649 (0.39)	1893 (0.11)	8570 (0.50)	5519 (0.32)	7264 (0.42)	11,114 (0.65)
Single-genotype (SG₄₅₄)	GS-FLX Titanium	1,241,260 (100)	6582 (0.53)	1826 (0.15)	11,070 (0.89)	10,463 (0.84)	86,828 (7.00)	21,849 (1.76)
July 8, 2008	Non-normalized	1,241,260 (100)	6582 (0.53)	1826 (0.15)	11,070 (0.89)	10,463 (0.84)	86,828 (7.00)	21,849 (1.76)
All datasets		2,962,628 (100)	13,288 (0.45)	3719 (0.13)	19,642 (0.66)	15,984 (0.54)	94,092 (3.18)	32,964 (1.11)

* For each dataset, the numbers of reads filtered using the SnoWhite pipeline (Figure 1, Step 3) are shown by sequence type.
^† GS-FLX Titanium is the Roche 454 sequencing platform.

ISSN: 1471-2164