| Variant ID: vg0327370831 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 27370831 |
| 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: 272. )
ATAATATATATTTAAGAAAAGTAAAAATAGGGGGAAACAGTGTGCGCAAGGATATATTCATACACTGACTTGAGAAACATGGCAAGGCTGTGTCCACACG[C/T]
TGAATTTAGATACATTCCATGTTCACGTTCACAAAATAATCTGGATTTTATAAATACCTAGAAATCCAAATCAATTGTTAAGCATGAACTTGTATAATAT
ATATTATACAAGTTCATGCTTAACAATTGATTTGGATTTCTAGGTATTTATAAAATCCAGATTATTTTGTGAACGTGAACATGGAATGTATCTAAATTCA[G/A]
CGTGTGGACACAGCCTTGCCATGTTTCTCAAGTCAGTGTATGAATATATCCTTGCGCACACTGTTTCCCCCTATTTTTACTTTTCTTAAATATATATTAT
| 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 | 99.80% | 0.10% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.70% | 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 | 100.00% | 0.00% | 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 | 94.80% | 4.20% | 1.04% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0327370831 | C -> T | LOC_Os03g48120.1 | 5_prime_UTR_variant ; 40.0bp to feature; MODIFIER | N | Average:61.739; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
| vg0327370831 | C -> T | LOC_Os03g48140.1 | downstream_gene_variant ; 4004.0bp to feature; MODIFIER | N | Average:61.739; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |