| Variant ID: vg0510478333 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478333 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTAGACACCAAAACCTCCATCTTCCAGGAACTCTTCTTCTGGGCTTGGGAAAAAATTGAGCAAGACTGAGTACAACCACCGTACTCAACAAGACACACCC[A/T]
CAAATGCAGAATAAATGCAAGGGAGTACAAAGGAGTTATACTATAAAGGGTTAGGGTTTGCAGTAAACAGCATTTAAAGATATTTAGTTGCTCAGAGCTA
TAGCTCTGAGCAACTAAATATCTTTAAATGCTGTTTACTGCAAACCCTAACCCTTTATAGTATAACTCCTTTGTACTCCCTTGCATTTATTCTGCATTTG[T/A]
GGGTGTGTCTTGTTGAGTACGGTGGTTGTACTCAGTCTTGCTCAATTTTTTCCCAAGCCCAGAAGAAGAGTTCCTGGAAGATGGAGGTTTTGGTGTCTAG
| 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 | 91.30% | 0.40% | 8.15% | 0.11% | NA |
| All Indica | 2759 | 90.10% | 0.70% | 8.99% | 0.18% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Aus | 269 | 51.30% | 0.00% | 48.70% | 0.00% | NA |
| Indica I | 595 | 92.40% | 0.00% | 6.89% | 0.67% | NA |
| Indica II | 465 | 99.10% | 0.00% | 0.86% | 0.00% | NA |
| Indica III | 913 | 83.80% | 0.00% | 16.21% | 0.00% | NA |
| Indica Intermediate | 786 | 90.30% | 2.50% | 7.00% | 0.13% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.60% | 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 | 96.70% | 0.00% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478333 | A -> T | LOC_Os05g18210.1 | downstream_gene_variant ; 1166.0bp to feature; MODIFIER | silent_mutation | Average:20.555; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| vg0510478333 | A -> T | LOC_Os05g18230.1 | downstream_gene_variant ; 2815.0bp to feature; MODIFIER | silent_mutation | Average:20.555; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| vg0510478333 | A -> T | LOC_Os05g18220.1 | intron_variant ; MODIFIER | silent_mutation | Average:20.555; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |
| vg0510478333 | A -> DEL | N | N | silent_mutation | Average:20.555; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 | N | N | N | N |