Table 4.
SNP validation comparison using a transcriptome dataset from polyploid wheat
| Original study |
Window 80, |
Window 80, |
Window 40, |
Window 10, |
|
|---|---|---|---|---|---|
| SNP score > 0 | SNP score > 0.25 | SNP score > 0 | SNP score > 0 | ||
| Validated SNPs |
64 |
40 (37) |
28 (22) |
35 (34) |
18 (23) |
| False-positives |
61 |
3 (6) |
1 (0) |
2 (1) |
3 (8) |
| False-positive rate | 49% | 7% (14%) | 3% (0%) | 5% (3%) | 14% (26%) |
The number of SNPs from the original study and from different settings using our strategy. There are multiple numbers per parameter explored. These reflect different alignment programs used under these settings. The first set of numbers were from Novoalign alignments, and the second were from Megablast (in parentheses).