| Variant ID: vg0135358029 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35358029 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 390. )
CTTGGGCACTCAGCGTTGTGTAAGATCCTGAGATCCCGAACCCATATATCTCCTCACTCCATGTATGAAAGATTGCTTCTTTCCTGAAATAATTTGAGAC[G/A]
TACACATTGGGAGATATGCCACAATCACCGGCAGCAGCAAGAACGTGTGAGCAAGGAAGGTGATGAAGCTTCGGCTTCATACAACTGCAGGTACATCCAC
GTGGATGTACCTGCAGTTGTATGAAGCCGAAGCTTCATCACCTTCCTTGCTCACACGTTCTTGCTGCTGCCGGTGATTGTGGCATATCTCCCAATGTGTA[C/T]
GTCTCAAATTATTTCAGGAAAGAAGCAATCTTTCATACATGGAGTGAGGAGATATATGGGTTCGGGATCTCAGGATCTTACACAACGCTGAGTGCCCAAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 38.70% | 2.10% | 32.61% | 26.56% | NA |
| All Indica | 2759 | 26.90% | 1.30% | 46.54% | 25.23% | NA |
| All Japonica | 1512 | 62.40% | 0.60% | 5.69% | 31.28% | NA |
| Aus | 269 | 3.00% | 20.10% | 52.04% | 24.91% | NA |
| Indica I | 595 | 19.20% | 0.70% | 63.53% | 16.64% | NA |
| Indica II | 465 | 19.10% | 1.90% | 51.18% | 27.74% | NA |
| Indica III | 913 | 35.70% | 0.80% | 33.41% | 30.12% | NA |
| Indica Intermediate | 786 | 27.10% | 2.20% | 46.18% | 24.55% | NA |
| Temperate Japonica | 767 | 55.40% | 0.10% | 2.74% | 41.72% | NA |
| Tropical Japonica | 504 | 63.90% | 1.60% | 11.71% | 22.82% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 2.49% | 15.77% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 4.17% | 3.12% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 30.00% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135358029 | G -> A | LOC_Os01g61090.1 | synonymous_variant ; p.Tyr772Tyr; LOW | synonymous_codon | Average:6.214; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |
| vg0135358029 | G -> DEL | LOC_Os01g61090.1 | N | frameshift_variant | Average:6.214; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |