| Variant ID: vg0108457578 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457578 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )
ACATACAAGCCTACATACGCCAAGACACGCCGCCGGATATCGACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATA[C/T]
GAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGGAGGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAG
CTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCCTCCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTC[G/A]
TATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTCGATATCCGGCGGCGTGTCTTGGCGTATGTAGGCTTGTATGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.30% | 0.00% | 2.52% | 12.19% | NA |
| All Indica | 2759 | 82.20% | 0.00% | 3.30% | 14.46% | NA |
| All Japonica | 1512 | 87.00% | 0.00% | 1.72% | 11.24% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 84.00% | 0.00% | 5.04% | 10.92% | NA |
| Indica II | 465 | 76.30% | 0.00% | 2.37% | 21.29% | NA |
| Indica III | 913 | 82.60% | 0.00% | 3.50% | 13.91% | NA |
| Indica Intermediate | 786 | 84.00% | 0.00% | 2.29% | 13.74% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.00% | 2.22% | NA |
| Tropical Japonica | 504 | 69.60% | 0.00% | 4.37% | 25.99% | NA |
| Japonica Intermediate | 241 | 89.20% | 0.00% | 1.66% | 9.13% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 2.22% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457578 | C -> T | LOC_Os01g15070.1 | synonymous_variant ; p.Tyr51Tyr; LOW | N | Average:55.391; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0108457578 | C -> T | LOC_Os01g15080.1 | upstream_gene_variant ; 381.0bp to feature; MODIFIER | N | Average:55.391; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0108457578 | C -> T | LOC_Os01g15090.1 | upstream_gene_variant ; 3494.0bp to feature; MODIFIER | N | Average:55.391; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |
| vg0108457578 | C -> T | LOC_Os01g15060.1 | downstream_gene_variant ; 1556.0bp to feature; MODIFIER | N | Average:55.391; most accessible tissue: Zhenshan97 root, score: 69.506 | N | N | N | N |