| Variant ID: vg0132053806 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 32053806 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 281. )
TTGTACCATGAGGGTAAGATAGAATATTGACAACCCGAACCTCACTGATACATACAACACTAGAGCAGGAAGGATCACATATCTAAATGTGCAGAAGTTT[C/T]
CAATTCTTAATCTTCTACAAATGAGTGCCGTGAAAGTAAATTTGTACCAGGTAAAATCACAAGATATATTATCTTAGCAAAGAAAAGCTTTAAAAAATAT
ATATTTTTTAAAGCTTTTCTTTGCTAAGATAATATATCTTGTGATTTTACCTGGTACAAATTTACTTTCACGGCACTCATTTGTAGAAGATTAAGAATTG[G/A]
AAACTTCTGCACATTTAGATATGTGATCCTTCCTGCTCTAGTGTTGTATGTATCAGTGAGGTTCGGGTTGTCAATATTCTATCTTACCCTCATGGTACAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 65.80% | 34.20% | 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0132053806 | C -> T | LOC_Os01g55620.1 | upstream_gene_variant ; 3040.0bp to feature; MODIFIER | silent_mutation | Average:41.845; most accessible tissue: Callus, score: 74.92 | N | N | N | N |
| vg0132053806 | C -> T | LOC_Os01g55640.1 | upstream_gene_variant ; 3349.0bp to feature; MODIFIER | silent_mutation | Average:41.845; most accessible tissue: Callus, score: 74.92 | N | N | N | N |
| vg0132053806 | C -> T | LOC_Os01g55650.1 | downstream_gene_variant ; 3577.0bp to feature; MODIFIER | silent_mutation | Average:41.845; most accessible tissue: Callus, score: 74.92 | N | N | N | N |
| vg0132053806 | C -> T | LOC_Os01g55630.1 | intron_variant ; MODIFIER | silent_mutation | Average:41.845; most accessible tissue: Callus, score: 74.92 | N | N | N | N |