| Variant ID: vg1125246115 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25246115 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.00, others allele: 0.00, population size: 359. )
ATTTCTCCAGAGCTAGCACCTAAAACCTTTTTCCGTTTCGGAGGAAATCAGCTCAGGTTTTCTGACGTGGCATGGTTACAACAAGGTTTCTTGCTTGTTT[C/A]
TGCAAGAGAAACCAGTCATGGTCCTCATGGAGTTCACCAAATTTACAATGACAGGCTTGGAGGCGACGAGAAGATGTCGGTGAAGGCTTTTTTTTACTGG
CCAGTAAAAAAAAGCCTTCACCGACATCTTCTCGTCGCCTCCAAGCCTGTCATTGTAAATTTGGTGAACTCCATGAGGACCATGACTGGTTTCTCTTGCA[G/T]
AAACAAGCAAGAAACCTTGTTGTAACCATGCCACGTCAGAAAACCTGAGCTGATTTCCTCCGAAACGGAAAAAGGTTTTAGGTGCTAGCTCTGGAGAAAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.00% | 3.90% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 95.10% | 4.90% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 81.80% | 18.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.60% | 6.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 93.60% | 6.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.00% | 4.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1125246115 | C -> A | LOC_Os11g41990.1 | 3_prime_UTR_variant ; 226.0bp to feature; MODIFIER | silent_mutation | Average:68.483; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | N | N | N | N |
| vg1125246115 | C -> A | LOC_Os11g41990.2 | 3_prime_UTR_variant ; 226.0bp to feature; MODIFIER | silent_mutation | Average:68.483; most accessible tissue: Zhenshan97 young leaf, score: 80.325 | N | N | N | N |