| Variant ID: vg0503844768 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 3844768 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATAAAAAAAGACAAATCCAACATACCCAAATTTATCATTTTTTATTTCTCAAAGTATAGATCGAGTTTCAATTTGATTTTTGTTGGGGTGATAGATATTT[C/T]
ATATTAATATACTCTACATTGTAGAAAAGCAGATTTTTTTTCACAACCATTTACATTAAATCTAAAGAAAGATCCCCGCAAAATTAAATCTAAAAGAAAG
CTTTCTTTTAGATTTAATTTTGCGGGGATCTTTCTTTAGATTTAATGTAAATGGTTGTGAAAAAAAATCTGCTTTTCTACAATGTAGAGTATATTAATAT[G/A]
AAATATCTATCACCCCAACAAAAATCAAATTGAAACTCGATCTATACTTTGAGAAATAAAAAATGATAAATTTGGGTATGTTGGATTTGTCTTTTTTTAT
| 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844768 | C -> T | LOC_Os05g07260.1 | downstream_gene_variant ; 1599.0bp to feature; MODIFIER | silent_mutation | Average:31.676; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
| vg0503844768 | C -> T | LOC_Os05g07260.2 | downstream_gene_variant ; 1610.0bp to feature; MODIFIER | silent_mutation | Average:31.676; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
| vg0503844768 | C -> T | LOC_Os05g07260.4 | downstream_gene_variant ; 1610.0bp to feature; MODIFIER | silent_mutation | Average:31.676; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
| vg0503844768 | C -> T | LOC_Os05g07260.3 | downstream_gene_variant ; 1599.0bp to feature; MODIFIER | silent_mutation | Average:31.676; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
| vg0503844768 | C -> T | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.676; most accessible tissue: Callus, score: 65.885 | N | N | N | N |