| Variant ID: vg0817015840 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17015840 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCAGCCACCAGCTGACAAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACAGCAGCTGAGAAATCAAGTACAAGATGAAGAACCCGA[G/T]
TGTAAGAAAGTTATTGTTTGTTACAACTGCAATGAAGAAGGGCATTACTCCAAAAACTGTCCCCAACCAAGGCAAAATCGACCTCCACATTACCGCCAAT
ATTGGCGGTAATGTGGAGGTCGATTTTGCCTTGGTTGGGGACAGTTTTTGGAGTAATGCCCTTCTTCATTGCAGTTGTAACAAACAATAACTTTCTTACA[C/A]
TCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTGCTGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTTGTCAGCTGGTGGCTGGG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.00% | 0.40% | 15.62% | 65.00% | NA |
| All Indica | 2759 | 2.70% | 0.60% | 14.53% | 82.17% | NA |
| All Japonica | 1512 | 52.20% | 0.00% | 11.64% | 36.18% | NA |
| Aus | 269 | 0.40% | 0.70% | 27.88% | 71.00% | NA |
| Indica I | 595 | 4.90% | 0.70% | 2.69% | 91.76% | NA |
| Indica II | 465 | 1.50% | 0.00% | 17.20% | 81.29% | NA |
| Indica III | 913 | 1.90% | 0.80% | 23.11% | 74.26% | NA |
| Indica Intermediate | 786 | 2.70% | 0.80% | 11.96% | 84.61% | NA |
| Temperate Japonica | 767 | 75.10% | 0.00% | 4.04% | 20.86% | NA |
| Tropical Japonica | 504 | 20.40% | 0.00% | 19.44% | 60.12% | NA |
| Japonica Intermediate | 241 | 45.60% | 0.00% | 19.50% | 34.85% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 67.71% | 22.92% | NA |
| Intermediate | 90 | 26.70% | 0.00% | 23.33% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0817015840 | G -> T | LOC_Os08g27910.1 | missense_variant ; p.Glu416Asp; MODERATE | nonsynonymous_codon ; E416D | Average:5.698; most accessible tissue: Callus, score: 10.152 | unknown | unknown | TOLERATED | 0.09 |
| vg0817015840 | G -> DEL | LOC_Os08g27910.1 | N | frameshift_variant | Average:5.698; most accessible tissue: Callus, score: 10.152 | N | N | N | N |