Variant ID: vg0503844815 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 3844815 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTCAAAGTATAGATCGAGTTTCAATTTGATTTTTGTTGGGGTGATAGATATTTCATATTAATATACTCTACATTGTAGAAAAGCAGATTTTTTTTCACAA[C/T]
CATTTACATTAAATCTAAAGAAAGATCCCCGCAAAATTAAATCTAAAAGAAAGATGTACAGAGGGGACATCTCTGGATTAGAATCCATTCCGTGGAATTA
TAATTCCACGGAATGGATTCTAATCCAGAGATGTCCCCTCTGTACATCTTTCTTTTAGATTTAATTTTGCGGGGATCTTTCTTTAGATTTAATGTAAATG[G/A]
TTGTGAAAAAAAATCTGCTTTTCTACAATGTAGAGTATATTAATATGAAATATCTATCACCCCAACAAAAATCAAATTGAAACTCGATCTATACTTTGAG
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 | 99.30% | 0.60% | 0.13% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 88.10% | 10.00% | 1.86% | 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 | 99.90% | 0.00% | 0.11% | 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 | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0503844815 | C -> T | LOC_Os05g07260.1 | downstream_gene_variant ; 1646.0bp to feature; MODIFIER | silent_mutation | Average:32.356; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
vg0503844815 | C -> T | LOC_Os05g07260.2 | downstream_gene_variant ; 1657.0bp to feature; MODIFIER | silent_mutation | Average:32.356; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
vg0503844815 | C -> T | LOC_Os05g07260.4 | downstream_gene_variant ; 1657.0bp to feature; MODIFIER | silent_mutation | Average:32.356; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
vg0503844815 | C -> T | LOC_Os05g07260.3 | downstream_gene_variant ; 1646.0bp to feature; MODIFIER | silent_mutation | Average:32.356; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
vg0503844815 | C -> T | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.356; most accessible tissue: Callus, score: 65.885 | N | N | N | N |