| Variant ID: vg1200352442 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 352442 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 304. )
CATTAATAAAATTTTGGGGGACCAAATTTAGTCTGCAACACCTACTCTCCTTTGGTTTATTCATTTCAAACATAGTGAGCTTAAGGCTACGTAACCTTGG[A/T]
ATTATTCTAAACAATCTTTATTACAGATCTAGCAAGTTCTTAATACTCTTGCTTCAACATAAGTTCTCTATACAACCTACACAGGATTCACCGATGCGTA
TACGCATCGGTGAATCCTGTGTAGGTTGTATAGAGAACTTATGTTGAAGCAAGAGTATTAAGAACTTGCTAGATCTGTAATAAAGATTGTTTAGAATAAT[T/A]
CCAAGGTTACGTAGCCTTAAGCTCACTATGTTTGAAATGAATAAACCAAAGGAGAGTAGGTGTTGCAGACTAAATTTGGTCCCCCAAAATTTTATTAATG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.10% | 0.70% | 0.28% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.20% | 0.10% | 0.66% | 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 | 99.80% | 0.00% | 0.22% | 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 | 99.70% | 0.00% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.80% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 68.80% | 29.20% | 2.08% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200352442 | A -> T | LOC_Os12g01574.1 | upstream_gene_variant ; 1797.0bp to feature; MODIFIER | silent_mutation | Average:59.103; most accessible tissue: Callus, score: 83.049 | N | N | N | N |
| vg1200352442 | A -> T | LOC_Os12g01570.1 | downstream_gene_variant ; 3297.0bp to feature; MODIFIER | silent_mutation | Average:59.103; most accessible tissue: Callus, score: 83.049 | N | N | N | N |
| vg1200352442 | A -> T | LOC_Os12g01590.1 | downstream_gene_variant ; 3081.0bp to feature; MODIFIER | silent_mutation | Average:59.103; most accessible tissue: Callus, score: 83.049 | N | N | N | N |
| vg1200352442 | A -> T | LOC_Os12g01580.1 | intron_variant ; MODIFIER | silent_mutation | Average:59.103; most accessible tissue: Callus, score: 83.049 | N | N | N | N |
| vg1200352442 | A -> T | LOC_Os12g01580.2 | intron_variant ; MODIFIER | silent_mutation | Average:59.103; most accessible tissue: Callus, score: 83.049 | N | N | N | N |