| Variant ID: vg0918112943 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 18112943 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 254. )
ATAGGTAGTAAGCATCTCAATCTGAGCTCAGCACCTATATTAATATAAATTCCTTTCTGTGTGGTAAAATAGTTTAACTCTTTGTTCGAATTTCAAACCC[T/C]
TTGATGGTTTTTAGGTAACAAAGCGAATACATAAGATCTTTGAAAAAGACCAAGTTGGTACATACTTCCTCCGTTTCACAATGTAAGACTTTCTAGCATT
AATGCTAGAAAGTCTTACATTGTGAAACGGAGGAAGTATGTACCAACTTGGTCTTTTTCAAAGATCTTATGTATTCGCTTTGTTACCTAAAAACCATCAA[A/G]
GGGTTTGAAATTCGAACAAAGAGTTAAACTATTTTACCACACAGAAAGGAATTTATATTAATATAGGTGCTGAGCTCAGATTGAGATGCTTACTACCTAT
| 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 | 99.70% | 0.30% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.30% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0918112943 | T -> C | LOC_Os09g29790.1 | upstream_gene_variant ; 3630.0bp to feature; MODIFIER | N | Average:27.756; most accessible tissue: Callus, score: 67.601 | N | N | N | N |
| vg0918112943 | T -> C | LOC_Os09g29810.1 | upstream_gene_variant ; 2182.0bp to feature; MODIFIER | N | Average:27.756; most accessible tissue: Callus, score: 67.601 | N | N | N | N |
| vg0918112943 | T -> C | LOC_Os09g29800.1 | intron_variant ; MODIFIER | N | Average:27.756; most accessible tissue: Callus, score: 67.601 | N | N | N | N |