| Variant ID: vg0234311101 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34311101 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAAGATAAAAGAACCCTCAATTATTGAATTCTATTCGAGAATCTCCATCCGAAATTTTCTTCATGTTGGTACAATTAGAATTGAGATGCAGAAATTTCTC[A/T]
CAATTTGATCCACATGCCTTTTCATAGGGTGTTTTTTTGCTACGTAGAGAAGATAATTACTTACGAATTCCAAGAATACCATTATCGGAACAACTCTGCG
CGCAGAGTTGTTCCGATAATGGTATTCTTGGAATTCGTAAGTAATTATCTTCTCTACGTAGCAAAAAAACACCCTATGAAAAGGCATGTGGATCAAATTG[T/A]
GAGAAATTTCTGCATCTCAATTCTAATTGTACCAACATGAAGAAAATTTCGGATGGAGATTCTCGAATAGAATTCAATAATTGAGGGTTCTTTTATCTTG
| 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 97.10% | 2.90% | 0.00% | 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 | 91.30% | 8.70% | 0.00% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0234311101 | A -> T | LOC_Os02g56040.1 | upstream_gene_variant ; 3372.0bp to feature; MODIFIER | silent_mutation | Average:34.03; most accessible tissue: Callus, score: 47.253 | N | N | N | N |
| vg0234311101 | A -> T | LOC_Os02g56060.1 | upstream_gene_variant ; 1605.0bp to feature; MODIFIER | silent_mutation | Average:34.03; most accessible tissue: Callus, score: 47.253 | N | N | N | N |
| vg0234311101 | A -> T | LOC_Os02g56050.1 | intron_variant ; MODIFIER | silent_mutation | Average:34.03; most accessible tissue: Callus, score: 47.253 | N | N | N | N |