| Variant ID: vg0817614367 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 17614367 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGTGCACTGCAGCTAGATTATACTCGTATTTATTTGTTGTGCTTTTAACTTTTTGTTTCCTTACAAGAAATAAAAAGAGGCTATGATCCTCTGATCATTA[C/T]
TATTAATCACACTACGAGTGACAAACTCGGAACAAGAATTATCGAAGCTCCTAACCATATTAATTATTTAATTATTATCAATTGAAATTTAAAATAGTAT
ATACTATTTTAAATTTCAATTGATAATAATTAAATAATTAATATGGTTAGGAGCTTCGATAATTCTTGTTCCGAGTTTGTCACTCGTAGTGTGATTAATA[G/A]
TAATGATCAGAGGATCATAGCCTCTTTTTATTTCTTGTAAGGAAACAAAAAGTTAAAAGCACAACAAATAAATACGAGTATAATCTAGCTGCAGTGCACG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 79.80% | 20.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 83.10% | 16.90% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 81.90% | 18.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 65.10% | 34.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0817614367 | C -> T | LOC_Os08g28790.1 | 3_prime_UTR_variant ; 169.0bp to feature; MODIFIER | silent_mutation | Average:64.858; most accessible tissue: Minghui63 young leaf, score: 78.821 | N | N | N | N |
| vg0817614367 | C -> T | LOC_Os08g28800.1 | upstream_gene_variant ; 3525.0bp to feature; MODIFIER | silent_mutation | Average:64.858; most accessible tissue: Minghui63 young leaf, score: 78.821 | N | N | N | N |