| Variant ID: vg0817015931 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015931 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTCCACAT[T/C]
ACCGCCAATTTACACGAAGCAGACATTCCAATCGTATTGTGGTCACTGGAGCAAACGCTGTACCCGTGAGGCCTCGTGTTAATCAGAACCCATAGCAGAA
TTCTGCTATGGGTTCTGATTAACACGAGGCCTCACGGGTACAGCGTTTGCTCCAGTGACCACAATACGATTGGAATGTCTGCTTCGTGTAAATTGGCGGT[A/G]
ATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 16.80% | 0.30% | 13.99% | 68.92% | NA |
| All Indica | 2759 | 1.70% | 0.50% | 9.42% | 88.37% | NA |
| All Japonica | 1512 | 47.80% | 0.00% | 15.08% | 37.10% | NA |
| Aus | 269 | 0.70% | 0.00% | 31.97% | 67.29% | NA |
| Indica I | 595 | 4.20% | 0.00% | 4.03% | 91.76% | NA |
| Indica II | 465 | 0.90% | 0.00% | 1.94% | 97.20% | NA |
| Indica III | 913 | 0.40% | 1.20% | 15.99% | 82.37% | NA |
| Indica Intermediate | 786 | 1.90% | 0.30% | 10.31% | 87.53% | NA |
| Temperate Japonica | 767 | 69.60% | 0.00% | 9.65% | 20.73% | NA |
| Tropical Japonica | 504 | 18.30% | 0.00% | 19.44% | 62.30% | NA |
| Japonica Intermediate | 241 | 40.20% | 0.00% | 23.24% | 36.51% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 72.92% | 26.04% | NA |
| Intermediate | 90 | 23.30% | 0.00% | 18.89% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015931 | T -> C | LOC_Os08g27910.1 | missense_variant ; p.Tyr447His; MODERATE | nonsynonymous_codon ; Y447H | Average:6.214; most accessible tissue: Callus, score: 15.831 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0817015931 | T -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:6.214; most accessible tissue: Callus, score: 15.831 | N | N | N | N |