| Variant ID: vg1001933465 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933465 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTTACAGTAGAATAGAAGTTTACCCAATCATTTTCATCTATGTCCGTAAAATATTCACGAACAATCAATGTCCTCTCCATTTTGAACTTTGCATGTGCTA[T/C]
TGATCCGCAGCTGCTATCTCCATTGATGTACAAAATAGAAGAAAAGTATGATCTGATCCGCTCATCATTGCAGACATGGCTGATCAAGGATTTCTTTCCT
AGGAAAGAAATCCTTGATCAGCCATGTCTGCAATGATGAGCGGATCAGATCATACTTTTCTTCTATTTTGTACATCAATGGAGATAGCAGCTGCGGATCA[A/G]
TAGCACATGCAAAGTTCAAAATGGAGAGGACATTGATTGTTCGTGAATATTTTACGGACATAGATGAAAATGATTGGGTAAACTTCTATTCTACTGTAAG
| 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 | 80.20% | 4.10% | 0.49% | 15.15% | NA |
| All Indica | 2759 | 70.80% | 6.60% | 0.62% | 21.96% | NA |
| All Japonica | 1512 | 99.00% | 0.50% | 0.00% | 0.46% | NA |
| Aus | 269 | 62.80% | 0.00% | 1.12% | 36.06% | NA |
| Indica I | 595 | 59.50% | 0.20% | 0.50% | 39.83% | NA |
| Indica II | 465 | 74.40% | 11.00% | 0.22% | 14.41% | NA |
| Indica III | 913 | 70.30% | 9.70% | 0.88% | 19.06% | NA |
| Indica Intermediate | 786 | 77.90% | 5.20% | 0.64% | 16.28% | NA |
| Temperate Japonica | 767 | 99.20% | 0.10% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 1.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 4.40% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933465 | T -> C | LOC_Os10g04160.1 | missense_variant ; p.Ile140Val; MODERATE | nonsynonymous_codon ; I140V | Average:39.946; most accessible tissue: Callus, score: 75.859 | unknown | unknown | TOLERATED | 0.27 |
| vg1001933465 | T -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:39.946; most accessible tissue: Callus, score: 75.859 | N | N | N | N |