| Variant ID: vg0503844727 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 3844727 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CATAAAATCCTAAGGCTTAATTCAACTCACACATTTTCGAAATAAAAAAAGACAAATCCAACATACCCAAATTTATCATTTTTTATTTCTCAAAGTATAG[A/T]
TCGAGTTTCAATTTGATTTTTGTTGGGGTGATAGATATTTCATATTAATATACTCTACATTGTAGAAAAGCAGATTTTTTTTCACAACCATTTACATTAA
TTAATGTAAATGGTTGTGAAAAAAAATCTGCTTTTCTACAATGTAGAGTATATTAATATGAAATATCTATCACCCCAACAAAAATCAAATTGAAACTCGA[T/A]
CTATACTTTGAGAAATAAAAAATGATAAATTTGGGTATGTTGGATTTGTCTTTTTTTATTTCGAAAATGTGTGAGTTGAATTAAGCCTTAGGATTTTATG
| 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 | 99.40% | 0.40% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.80% | 0.18% | 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 | 99.30% | 0.30% | 0.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.30% | 2.30% | 0.38% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0503844727 | A -> T | LOC_Os05g07260.1 | downstream_gene_variant ; 1558.0bp to feature; MODIFIER | silent_mutation | Average:31.976; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
| vg0503844727 | A -> T | LOC_Os05g07260.2 | downstream_gene_variant ; 1569.0bp to feature; MODIFIER | silent_mutation | Average:31.976; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
| vg0503844727 | A -> T | LOC_Os05g07260.4 | downstream_gene_variant ; 1569.0bp to feature; MODIFIER | silent_mutation | Average:31.976; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
| vg0503844727 | A -> T | LOC_Os05g07260.3 | downstream_gene_variant ; 1558.0bp to feature; MODIFIER | silent_mutation | Average:31.976; most accessible tissue: Callus, score: 65.885 | N | N | N | N |
| vg0503844727 | A -> T | LOC_Os05g07270.1 | intron_variant ; MODIFIER | silent_mutation | Average:31.976; most accessible tissue: Callus, score: 65.885 | N | N | N | N |