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 |
Unique |
Coastal |
Yakima |
Interior |
Total† |
|
| --------------- All isotigs (1 isotig/isogroup (I1)) -------------- | ||||||||
| Multi-genotype #1 (MG1SANG) |
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 (MG2IL) |
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 (CBIL) |
Coastal |
Illumina |
13.41 |
1044 (895) |
66,304 (56,547) |
29,051 (24,703) |
53,275 (45,437) |
66,304 (56,547) |
| Yakima (YKIL) |
Yakima |
Illumina |
8.99 |
638 (545) |
43,066 (36,621) |
- |
40,840 (34,750) |
47,573 (40,505) |
| Interior (INTIL) |
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 CBIL dataset, 29,051 of which were detected in the YKIL dataset and 53,275 of which were detected in the INTIL dataset.