| Variant ID: vg0521976361 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21976361 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 86. )
TCAGAAAGAACCCCTCCATTTTAAAAAATGAGTATATACAATCATCTAACAAAGTTCAGAACAAAGCTCCCCATATTTTTTTGTTAGTAGTACAACATAT[A/T]
TTTTTTTAAAATTTGCAGTAAGTACTGATTATAAATTAGGTTGTTTTTTGTAAACTACATTTTCAGTTAGTAGTAGTATATGCTATTTTTAAATATAGTG
CACTATATTTAAAAATAGCATATACTACTACTAACTGAAAATGTAGTTTACAAAAAACAACCTAATTTATAATCAGTACTTACTGCAAATTTTAAAAAAA[T/A]
ATATGTTGTACTACTAACAAAAAAATATGGGGAGCTTTGTTCTGAACTTTGTTAGATGATTGTATATACTCATTTTTTAAAATGGAGGGGTTCTTTCTGA
| 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 | 38.70% | 6.10% | 11.68% | 43.55% | NA |
| All Indica | 2759 | 2.90% | 10.00% | 18.09% | 69.08% | NA |
| All Japonica | 1512 | 98.60% | 0.10% | 0.46% | 0.79% | NA |
| Aus | 269 | 45.00% | 1.10% | 14.13% | 39.78% | NA |
| Indica I | 595 | 1.70% | 15.10% | 11.09% | 72.10% | NA |
| Indica II | 465 | 3.20% | 2.20% | 12.69% | 81.94% | NA |
| Indica III | 913 | 1.50% | 11.90% | 26.18% | 60.35% | NA |
| Indica Intermediate | 786 | 5.10% | 8.40% | 17.18% | 69.34% | NA |
| Temperate Japonica | 767 | 98.70% | 0.10% | 0.13% | 1.04% | NA |
| Tropical Japonica | 504 | 99.00% | 0.20% | 0.40% | 0.40% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 1.66% | 0.83% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 50.00% | 6.70% | 8.89% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521976361 | A -> T | LOC_Os05g37550.1 | downstream_gene_variant ; 3726.0bp to feature; MODIFIER | silent_mutation | Average:5.809; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |
| vg0521976361 | A -> T | LOC_Os05g37540.1 | intron_variant ; MODIFIER | silent_mutation | Average:5.809; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |
| vg0521976361 | A -> DEL | N | N | silent_mutation | Average:5.809; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |