| Variant ID: vg0123775878 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 23775878 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGAAGAAGTCATTGTAGAAAAATCTCAATGAGTGAAATAGCTTAGATCGTAAGAATACTCACAAATTAATGCATACCCTAGAGTTTTTTTTTTTGAAATA[C/T]
ACAAAAGACTTGCATATCATTGCATTAAGAGGAGTAAAGTAATACAAGACAGACAGAGAAGAACAGGGAGGAGAGAGGAGGGGAGGAGAAAAGGAGAAAC
GTTTCTCCTTTTCTCCTCCCCTCCTCTCTCCTCCCTGTTCTTCTCTGTCTGTCTTGTATTACTTTACTCCTCTTAATGCAATGATATGCAAGTCTTTTGT[G/A]
TATTTCAAAAAAAAAAACTCTAGGGTATGCATTAATTTGTGAGTATTCTTACGATCTAAGCTATTTCACTCATTGAGATTTTTCTACAATGACTTCTTCT
| 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 | 42.90% | 1.70% | 1.93% | 53.47% | NA |
| All Indica | 2759 | 11.10% | 0.00% | 3.04% | 85.79% | NA |
| All Japonica | 1512 | 87.20% | 5.20% | 0.13% | 7.41% | NA |
| Aus | 269 | 92.20% | 0.00% | 1.12% | 6.69% | NA |
| Indica I | 595 | 4.20% | 0.00% | 2.69% | 93.11% | NA |
| Indica II | 465 | 6.90% | 0.00% | 3.87% | 89.25% | NA |
| Indica III | 913 | 12.40% | 0.00% | 1.75% | 85.87% | NA |
| Indica Intermediate | 786 | 17.40% | 0.10% | 4.33% | 78.12% | NA |
| Temperate Japonica | 767 | 99.30% | 0.30% | 0.00% | 0.39% | NA |
| Tropical Japonica | 504 | 73.80% | 6.20% | 0.40% | 19.64% | NA |
| Japonica Intermediate | 241 | 76.80% | 19.10% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 64.40% | 1.10% | 2.22% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0123775878 | C -> T | LOC_Os01g41930.1 | 5_prime_UTR_variant ; 624.0bp to feature; MODIFIER | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775878 | C -> T | LOC_Os01g41920.1 | upstream_gene_variant ; 3195.0bp to feature; MODIFIER | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775878 | C -> T | LOC_Os01g41910.1 | downstream_gene_variant ; 4363.0bp to feature; MODIFIER | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |
| vg0123775878 | C -> DEL | N | N | silent_mutation | Average:10.918; most accessible tissue: Callus, score: 62.341 | N | N | N | N |