| Variant ID: vg0525045469 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 25045469 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTCTTGGCTTCTTGAACTAAAGAAGTGCAAGGCAAATGTATTGCTTTGCTGTGTAGTATTCGTTTTCCTTTACCGGATCTGGTATAAATTAGAGGAAATC[A/T]
TGTCATTCGCTTGAATGAAATTTGTCAAATTTCTCGTAAACAACCTTTGCGGGCAATGTTGGTATGATTTCTCAATAGAAATTTTGTCATTCAACCAAGG
CCTTGGTTGAATGACAAAATTTCTATTGAGAAATCATACCAACATTGCCCGCAAAGGTTGTTTACGAGAAATTTGACAAATTTCATTCAAGCGAATGACA[T/A]
GATTTCCTCTAATTTATACCAGATCCGGTAAAGGAAAACGAATACTACACAGCAAAGCAATACATTTGCCTTGCACTTCTTTAGTTCAAGAAGCCAAGAA
| 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 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 1.90% | 98.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.10% | 5.90% | 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 | 90.60% | 9.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 10.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0525045469 | A -> T | LOC_Os05g43140.1 | 3_prime_UTR_variant ; 238.0bp to feature; MODIFIER | silent_mutation | Average:47.342; most accessible tissue: Callus, score: 89.172 | N | N | N | N |
| vg0525045469 | A -> T | LOC_Os05g43130.1 | upstream_gene_variant ; 1976.0bp to feature; MODIFIER | silent_mutation | Average:47.342; most accessible tissue: Callus, score: 89.172 | N | N | N | N |
| vg0525045469 | A -> T | LOC_Os05g43150.1 | upstream_gene_variant ; 919.0bp to feature; MODIFIER | silent_mutation | Average:47.342; most accessible tissue: Callus, score: 89.172 | N | N | N | N |