| Variant ID: vg1126903414 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903414 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 35. )
AATAGAAAATATTCTCTTAATAGGCTGGACGACGAGTGATGTCCATGTGGCTGATAACGGGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATC[C/T]
CTGAACTTTTCAGCCTGCCTCCCGGCCATCACCAACCTGTACATGGCGCTATTGTCCTGGCATGCCATCACAAGCTCGTGCGCCTCCCGGAGCGTGTCGT
ACGACACGCTCCGGGAGGCGCACGAGCTTGTGATGGCATGCCAGGACAATAGCGCCATGTACAGGTTGGTGATGGCCGGGAGGCAGGCTGAAAAGTTCAG[G/A]
GATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCCCGTTATCAGCCACATGGACATCACTCGTCGTCCAGCCTATTAAGAGAATATTTTCTATT
| 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 | 46.80% | 18.20% | 3.85% | 31.17% | NA |
| All Indica | 2759 | 47.10% | 9.60% | 3.30% | 40.01% | NA |
| All Japonica | 1512 | 41.40% | 36.40% | 3.84% | 18.39% | NA |
| Aus | 269 | 60.20% | 12.30% | 8.92% | 18.59% | NA |
| Indica I | 595 | 33.10% | 16.30% | 3.19% | 47.39% | NA |
| Indica II | 465 | 61.70% | 4.30% | 0.22% | 33.76% | NA |
| Indica III | 913 | 50.20% | 3.20% | 4.71% | 41.95% | NA |
| Indica Intermediate | 786 | 45.50% | 15.00% | 3.56% | 35.88% | NA |
| Temperate Japonica | 767 | 19.70% | 63.50% | 2.22% | 14.60% | NA |
| Tropical Japonica | 504 | 69.00% | 3.00% | 6.55% | 21.43% | NA |
| Japonica Intermediate | 241 | 52.70% | 19.90% | 3.32% | 24.07% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 3.12% | 12.50% | NA |
| Intermediate | 90 | 46.70% | 14.40% | 6.67% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903414 | C -> T | LOC_Os11g44460.1 | synonymous_variant ; p.Arg87Arg; LOW | synonymous_codon | Average:14.561; most accessible tissue: Callus, score: 46.436 | N | N | N | N |
| vg1126903414 | C -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:14.561; most accessible tissue: Callus, score: 46.436 | N | N | N | N |