| Variant ID: vg0108457619 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 8457619 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: Unkown |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 259. )
GACTTGAAGGATAGGCATGGCTATTCCCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTCGCCGGGCACAGATTCGAGG[A/T]
GGAAGACTACCCTGTTGTCGACTACGAGTCAGACCTTCAGACCGACATGTCCACAACAGTTAGATAGGCTACCCACATATTGTACTGGTGTGATTATGGT
ACCATAATCACACCAGTACAATATGTGGGTAGCCTATCTAACTGTTGTGGACATGTCGGTCTGAAGGTCTGACTCGTAGTCGACAACAGGGTAGTCTTCC[T/A]
CCTCGAATCTGTGCCCGGCGAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGGGAATAGCCATGCCTATCCTTCAAGTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 85.90% | 0.00% | 7.30% | 6.81% | NA |
| All Indica | 2759 | 81.00% | 0.00% | 10.80% | 8.16% | NA |
| All Japonica | 1512 | 91.10% | 0.00% | 2.58% | 6.28% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 88.70% | 0.00% | 9.24% | 2.02% | NA |
| Indica II | 465 | 84.10% | 0.00% | 9.03% | 6.88% | NA |
| Indica III | 913 | 72.10% | 0.00% | 14.13% | 13.80% | NA |
| Indica Intermediate | 786 | 83.80% | 0.00% | 9.16% | 7.00% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.39% | 1.43% | NA |
| Tropical Japonica | 504 | 79.60% | 0.00% | 5.95% | 14.48% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 2.49% | 4.56% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 0.00% | 6.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457619 | A -> T | LOC_Os01g15070.1 | missense_variant ; p.Glu65Val; MODERATE | N | Average:52.432; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0108457619 | A -> T | LOC_Os01g15080.1 | upstream_gene_variant ; 340.0bp to feature; MODIFIER | N | Average:52.432; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0108457619 | A -> T | LOC_Os01g15090.1 | upstream_gene_variant ; 3453.0bp to feature; MODIFIER | N | Average:52.432; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |
| vg0108457619 | A -> T | LOC_Os01g15060.1 | downstream_gene_variant ; 1597.0bp to feature; MODIFIER | N | Average:52.432; most accessible tissue: Zhenshan97 panicle, score: 68.538 | N | N | N | N |