| Variant ID: vg0727002546 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 27002546 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 295. )
ATGTCAATGTTCGTGCTCTGTGTGGATTGCTCTGAAATCAAGCACTACAGAAGTTTGGTCAAAGCTGGGTATGGTGTTTACGCTCAAGTGGGGAAGGTTG[C/T]
GGATCATGAATGCATGCCTACGGAGGTTTTGCCTGGGCAAAAAAGTCTGTCATCTAAATTTCCTGCTCAGTATCTCTCCTATCGCCTTAAGGATGAGCAT
ATGCTCATCCTTAAGGCGATAGGAGAGATACTGAGCAGGAAATTTAGATGACAGACTTTTTTGCCCAGGCAAAACCTCCGTAGGCATGCATTCATGATCC[G/A]
CAACCTTCCCCACTTGAGCGTAAACACCATACCCAGCTTTGACCAAACTTCTGTAGTGCTTGATTTCAGAGCAATCCACACAGAGCACGAACATTGACAT
| 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 | 99.20% | 0.60% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 1.10% | 0.25% | 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 | 98.10% | 0.90% | 1.08% | 0.00% | NA |
| Indica III | 913 | 97.30% | 2.50% | 0.22% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0727002546 | C -> T | LOC_Os07g45250.1 | missense_variant ; p.Ala161Val; MODERATE | N | Average:60.715; most accessible tissue: Callus, score: 88.336 | N | N | N | N |
| vg0727002546 | C -> T | LOC_Os07g45194.1 | upstream_gene_variant ; 1520.0bp to feature; MODIFIER | N | Average:60.715; most accessible tissue: Callus, score: 88.336 | N | N | N | N |
| vg0727002546 | C -> T | LOC_Os07g45260.1 | upstream_gene_variant ; 4077.0bp to feature; MODIFIER | N | Average:60.715; most accessible tissue: Callus, score: 88.336 | N | N | N | N |