Skip to main content

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

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

    No. of reads (× 106) No. of unique or shared SNPs*
Plant materials (dataset ID) Seed source Sequencing platform 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 (MG2 454) Coastal Roche 454       
Single-genotype (SG 454 ) 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      
  1. *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.
  2. 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.