| Variant ID: vg0817015851 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015851 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GCTGACAAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAG[T/C]
TATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTCCACATTACCGCCAATTTACACGAAGC
GCTTCGTGTAAATTGGCGGTAATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATA[A/G]
CTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTTGTCAGC
| 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 | 21.60% | 0.40% | 16.38% | 61.64% | NA |
| All Indica | 2759 | 4.40% | 0.60% | 15.88% | 79.12% | NA |
| All Japonica | 1512 | 56.30% | 0.00% | 8.93% | 34.72% | NA |
| Aus | 269 | 1.10% | 0.70% | 46.10% | 52.04% | NA |
| Indica I | 595 | 5.00% | 0.70% | 4.03% | 90.25% | NA |
| Indica II | 465 | 1.70% | 0.00% | 15.91% | 82.37% | NA |
| Indica III | 913 | 5.00% | 0.70% | 26.51% | 67.80% | NA |
| Indica Intermediate | 786 | 4.70% | 0.90% | 12.47% | 81.93% | NA |
| Temperate Japonica | 767 | 78.00% | 0.00% | 2.09% | 19.95% | NA |
| Tropical Japonica | 504 | 24.40% | 0.00% | 17.86% | 57.74% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.00% | 12.03% | 33.61% | NA |
| VI/Aromatic | 96 | 15.60% | 0.00% | 62.50% | 21.88% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 18.89% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015851 | T -> C | LOC_Os08g27910.1 | missense_variant ; p.Val420Ala; MODERATE | nonsynonymous_codon ; V420A | Average:5.698; most accessible tissue: Callus, score: 10.152 | unknown | unknown | TOLERATED | 0.07 |
| vg0817015851 | T -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.698; most accessible tissue: Callus, score: 10.152 | N | N | N | N |