| Variant ID: vg0817015895 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015895 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCCAATACAGCAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAA[A/G]
ACTGTCCCCAACCAAGGCAAAATCGACCTCCACATTACCGCCAATTTACACGAAGCAGACATTCCAATCGTATTGTGGTCACTGGAGCAAACGCTGTACC
GGTACAGCGTTTGCTCCAGTGACCACAATACGATTGGAATGTCTGCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGT[T/C]
TTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTGCTGTATTGGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.20% | 0.10% | 19.15% | 50.53% | NA |
| All Indica | 2759 | 12.60% | 0.10% | 25.23% | 62.05% | NA |
| All Japonica | 1512 | 62.90% | 0.10% | 4.03% | 33.00% | NA |
| Aus | 269 | 20.10% | 0.00% | 36.43% | 43.49% | NA |
| Indica I | 595 | 6.90% | 0.00% | 9.41% | 83.70% | NA |
| Indica II | 465 | 2.80% | 0.00% | 25.16% | 72.04% | NA |
| Indica III | 913 | 23.00% | 0.30% | 34.94% | 41.73% | NA |
| Indica Intermediate | 786 | 10.70% | 0.00% | 25.95% | 63.36% | NA |
| Temperate Japonica | 767 | 79.80% | 0.00% | 1.17% | 19.04% | NA |
| Tropical Japonica | 504 | 35.90% | 0.20% | 9.13% | 54.76% | NA |
| Japonica Intermediate | 241 | 65.60% | 0.00% | 2.49% | 31.95% | NA |
| VI/Aromatic | 96 | 39.60% | 0.00% | 39.58% | 20.83% | NA |
| Intermediate | 90 | 41.10% | 1.10% | 13.33% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015895 | A -> G | LOC_Os08g27910.1 | missense_variant ; p.Asn435Asp; MODERATE | nonsynonymous_codon | Average:5.698; most accessible tissue: Callus, score: 10.152 | unknown | unknown | TOLERATED | 1.00 |
| vg0817015895 | A -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.698; most accessible tissue: Callus, score: 10.152 | N | N | N | N |