| Variant ID: vg0825763345 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25763345 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 277. )
TACCCTTATAATGGGAAGATTTACTTGGGGCTCGCGGCGGCGAATTTGACGGGGAAGAATGACATGGTCGCCGTCGGTGAGCTCTACCGGAAGCTGCTGC[C/T]
GGCGGTGCAGAAGACGGATACCTACGGAGGAGTGATGCTTTGGAACAGCTACTATGACTCCATCACTCACTACGGACGGTATGTCAGTGCCTGGGCTTAA
TTAAGCCCAGGCACTGACATACCGTCCGTAGTGAGTGATGGAGTCATAGTAGCTGTTCCAAAGCATCACTCCTCCGTAGGTATCCGTCTTCTGCACCGCC[G/A]
GCAGCAGCTTCCGGTAGAGCTCACCGACGGCGACCATGTCATTCTTCCCCGTCAAATTCGCCGCCGCGAGCCCCAAGTAAATCTTCCCATTATAAGGGTA
| 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 | 99.70% | 0.20% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.10% | 0.70% | 0.26% | 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 | 100.00% | 0.00% | 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 | 97.20% | 2.00% | 0.79% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0825763345 | C -> T | LOC_Os08g40690.1 | missense_variant ; p.Pro283Leu; MODERATE | N | Average:71.382; most accessible tissue: Minghui63 panicle, score: 86.012 | N | N | N | N |
| vg0825763345 | C -> T | LOC_Os08g40680.1 | upstream_gene_variant ; 3396.0bp to feature; MODIFIER | N | Average:71.382; most accessible tissue: Minghui63 panicle, score: 86.012 | N | N | N | N |
| vg0825763345 | C -> T | LOC_Os08g40700.1 | upstream_gene_variant ; 1628.0bp to feature; MODIFIER | N | Average:71.382; most accessible tissue: Minghui63 panicle, score: 86.012 | N | N | N | N |
| vg0825763345 | C -> T | LOC_Os08g40710.1 | downstream_gene_variant ; 4204.0bp to feature; MODIFIER | N | Average:71.382; most accessible tissue: Minghui63 panicle, score: 86.012 | N | N | N | N |