| Variant ID: vg0136518492 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36518492 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGGGAGCTCTGCAGCCATGTTTTTCTGAAATAAACCATGGATAAAAATGAATGTCAGATTTGGTGGGGTGAGATGCTTAATTATTCTGGAAGAAGAATG[A/G]
TACTTACTCTAATGATGCATCGTCAGAAATAGACATTATATAGGAATACAGGTCGTCAGCAATCCTGGATTCCAGCCTCTCCGTTGAGCATTGCTTTGAC
GTCAAAGCAATGCTCAACGGAGAGGCTGGAATCCAGGATTGCTGACGACCTGTATTCCTATATAATGTCTATTTCTGACGATGCATCATTAGAGTAAGTA[T/C]
CATTCTTCTTCCAGAATAATTAAGCATCTCACCCCACCAAATCTGACATTCATTTTTATCCATGGTTTATTTCAGAAAAACATGGCTGCAGAGCTCCCAT
| 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 | 35.20% | 0.90% | 4.91% | 58.95% | NA |
| All Indica | 2759 | 1.90% | 1.10% | 4.06% | 92.93% | NA |
| All Japonica | 1512 | 96.50% | 0.70% | 0.13% | 2.65% | NA |
| Aus | 269 | 2.20% | 0.00% | 42.01% | 55.76% | NA |
| Indica I | 595 | 0.80% | 0.20% | 4.87% | 94.12% | NA |
| Indica II | 465 | 2.40% | 0.40% | 1.94% | 95.27% | NA |
| Indica III | 913 | 1.30% | 0.30% | 3.61% | 94.74% | NA |
| Indica Intermediate | 786 | 3.20% | 3.10% | 5.22% | 88.55% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.13% | 1.17% | NA |
| Tropical Japonica | 504 | 94.60% | 2.20% | 0.20% | 2.98% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.00% | 6.64% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 1.04% | 6.25% | NA |
| Intermediate | 90 | 64.40% | 2.20% | 4.44% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0136518492 | A -> G | LOC_Os01g63040.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:4.903; most accessible tissue: Callus, score: 9.262 | N | N | N | N |
| vg0136518492 | A -> G | LOC_Os01g63030.1 | downstream_gene_variant ; 1879.0bp to feature; MODIFIER | silent_mutation | Average:4.903; most accessible tissue: Callus, score: 9.262 | N | N | N | N |
| vg0136518492 | A -> DEL | N | N | silent_mutation | Average:4.903; most accessible tissue: Callus, score: 9.262 | N | N | N | N |