| Variant ID: vg1117780042 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17780042 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 268. )
GCTGGACGCCCTCGACGTCTCTATTATGAGTTGCTGGATTTTGTAAGTATATCGTTCAGTTAGATTTCTTACTATACGTCTCCTTTAATTAATTAGGTCC[T/A]
TGTATATAAGTAGACTATATATAGAAAATAATATACTCCCTTTTATCGTTGTAGAATGGAGATTCAAAGGGCCCGACGGCGGAGGGTTTTCGATACTGGA
TCCAGTATCGAAAACCCTCCGCCGTCGGGCCCTTTGAATCTCCATTCTACAACGATAAAAGGGAGTATATTATTTTCTATATATAGTCTACTTATATACA[A/T]
GGACCTAATTAATTAAAGGAGACGTATAGTAAGAAATCTAACTGAACGATATACTTACAAAATCCAGCAACTCATAATAGAGACGTCGAGGGCGTCCAGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 25.80% | 1.10% | 2.54% | 70.61% | NA |
| All Indica | 2759 | 10.40% | 0.10% | 2.54% | 87.02% | NA |
| All Japonica | 1512 | 54.80% | 0.10% | 1.72% | 43.39% | NA |
| Aus | 269 | 11.90% | 0.00% | 6.69% | 81.41% | NA |
| Indica I | 595 | 8.10% | 0.00% | 4.03% | 87.90% | NA |
| Indica II | 465 | 25.20% | 0.00% | 2.58% | 72.26% | NA |
| Indica III | 913 | 4.60% | 0.00% | 1.75% | 93.65% | NA |
| Indica Intermediate | 786 | 10.10% | 0.30% | 2.29% | 87.40% | NA |
| Temperate Japonica | 767 | 63.90% | 0.00% | 1.83% | 34.29% | NA |
| Tropical Japonica | 504 | 28.20% | 0.20% | 2.18% | 69.44% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.41% | 17.84% | NA |
| VI/Aromatic | 96 | 47.90% | 42.70% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 28.90% | 6.70% | 5.56% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117780042 | T -> A | LOC_Os11g30552.1 | intron_variant ; MODIFIER | silent_mutation | Average:6.331; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |
| vg1117780042 | T -> DEL | N | N | silent_mutation | Average:6.331; most accessible tissue: Minghui63 young leaf, score: 12.713 | N | N | N | N |