| Variant ID: vg1001933464 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933464 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ACTTACAGTAGAATAGAAGTTTACCCAATCATTTTCATCTATGTCCGTAAAATATTCACGAACAATCAATGTCCTCTCCATTTTGAACTTTGCATGTGCT[A/G]
TTGATCCGCAGCTGCTATCTCCATTGATGTACAAAATAGAAGAAAAGTATGATCTGATCCGCTCATCATTGCAGACATGGCTGATCAAGGATTTCTTTCC
GGAAAGAAATCCTTGATCAGCCATGTCTGCAATGATGAGCGGATCAGATCATACTTTTCTTCTATTTTGTACATCAATGGAGATAGCAGCTGCGGATCAA[T/C]
AGCACATGCAAAGTTCAAAATGGAGAGGACATTGATTGTTCGTGAATATTTTACGGACATAGATGAAAATGATTGGGTAAACTTCTATTCTACTGTAAGT
| 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 | 84.20% | 0.60% | 0.47% | 14.79% | NA |
| All Indica | 2759 | 78.20% | 0.00% | 0.40% | 21.38% | NA |
| All Japonica | 1512 | 97.40% | 1.70% | 0.53% | 0.40% | NA |
| Aus | 269 | 64.30% | 0.00% | 1.12% | 34.57% | NA |
| Indica I | 595 | 60.80% | 0.00% | 0.50% | 38.66% | NA |
| Indica II | 465 | 85.60% | 0.00% | 0.22% | 14.19% | NA |
| Indica III | 913 | 80.60% | 0.00% | 0.33% | 19.06% | NA |
| Indica Intermediate | 786 | 84.20% | 0.00% | 0.51% | 15.27% | NA |
| Temperate Japonica | 767 | 95.30% | 3.10% | 1.04% | 0.52% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933464 | A -> G | LOC_Os10g04160.1 | missense_variant ; p.Ile140Thr; MODERATE | nonsynonymous_codon ; I140T | Average:40.007; most accessible tissue: Callus, score: 75.859 | unknown | unknown | TOLERATED | 0.12 |
| vg1001933464 | A -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:40.007; most accessible tissue: Callus, score: 75.859 | N | N | N | N |