| Variant ID: vg0817614363 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17614363 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CTCCCGTGCACTGCAGCTAGATTATACTCGTATTTATTTGTTGTGCTTTTAACTTTTTGTTTCCTTACAAGAAATAAAAAGAGGCTATGATCCTCTGATC[A/G]
TTACTATTAATCACACTACGAGTGACAAACTCGGAACAAGAATTATCGAAGCTCCTAACCATATTAATTATTTAATTATTATCAATTGAAATTTAAAATA
TATTTTAAATTTCAATTGATAATAATTAAATAATTAATATGGTTAGGAGCTTCGATAATTCTTGTTCCGAGTTTGTCACTCGTAGTGTGATTAATAGTAA[T/C]
GATCAGAGGATCATAGCCTCTTTTTATTTCTTGTAAGGAAACAAAAAGTTAAAAGCACAACAAATAAATACGAGTATAATCTAGCTGCAGTGCACGGGAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 92.80% | 7.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 87.90% | 12.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 94.30% | 5.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 82.00% | 18.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 82.80% | 17.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 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 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0817614363 | A -> G | LOC_Os08g28790.1 | 3_prime_UTR_variant ; 165.0bp to feature; MODIFIER | silent_mutation | Average:65.162; most accessible tissue: Minghui63 young leaf, score: 79.191 | N | N | N | N |
| vg0817614363 | A -> G | LOC_Os08g28800.1 | upstream_gene_variant ; 3529.0bp to feature; MODIFIER | silent_mutation | Average:65.162; most accessible tissue: Minghui63 young leaf, score: 79.191 | N | N | N | N |