| Variant ID: vg0904847226 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 4847226 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )
GGGGACAGTTTTTGGAGTAATGCCCTTCTTCACTGCAGTTGTAACAAACAATAACTTTCTTACACTCGGGTTCTTCATCTTGTACTTGATTTCTCAGCTG[C/G]
TGTATTGGAACTTCCAAAGGTACAACGCAGATACTGGCCTCTGTCTTGTCAGCTGGTGGCTGGGGCTGAAATTGAGCATTGACACCTTGTGGTAGTGCAC
GTGCACTACCACAAGGTGTCAATGCTCAATTTCAGCCCCAGCCACCAGCTGACAAGACAGAGGCCAGTATCTGCGTTGTACCTTTGGAAGTTCCAATACA[G/C]
CAGCTGAGAAATCAAGTACAAGATGAAGAACCCGAGTGTAAGAAAGTTATTGTTTGTTACAACTGCAGTGAAGAAGGGCATTACTCCAAAAACTGTCCCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.00% | 0.00% | 3.32% | 73.59% | NA |
| All Indica | 2759 | 8.20% | 0.00% | 3.44% | 88.37% | NA |
| All Japonica | 1512 | 46.20% | 0.10% | 2.84% | 50.86% | NA |
| Aus | 269 | 22.70% | 0.00% | 1.86% | 75.46% | NA |
| Indica I | 595 | 8.60% | 0.00% | 3.19% | 88.24% | NA |
| Indica II | 465 | 7.30% | 0.00% | 1.94% | 90.75% | NA |
| Indica III | 913 | 5.80% | 0.00% | 4.27% | 89.92% | NA |
| Indica Intermediate | 786 | 11.20% | 0.00% | 3.56% | 85.24% | NA |
| Temperate Japonica | 767 | 49.50% | 0.00% | 1.56% | 48.89% | NA |
| Tropical Japonica | 504 | 32.30% | 0.00% | 4.56% | 63.10% | NA |
| Japonica Intermediate | 241 | 64.30% | 0.80% | 3.32% | 31.54% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 7.29% | 13.54% | NA |
| Intermediate | 90 | 31.10% | 0.00% | 7.78% | 61.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0904847226 | C -> G | LOC_Os09g09070.1 | missense_variant ; p.Gln404His; MODERATE | nonsynonymous_codon ; Q404H | Average:4.451; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0904847226 | C -> DEL | LOC_Os09g09070.1 | N | frameshift_variant | Average:4.451; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |