| Variant ID: vg0114587475 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14587475 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )
GAAGCGGTTAAATAAGCTTTTTTTTTTATTGCTGAAGAGTACATTAATTTAAGTGTTGCATTCATGGTAAGAACAAGAACAACTATACAGAGTTTTTGTA[T/C]
GTACGAAGTTGAGTACTCACATATGTCAACGTCATTTACCTAGACAAATTTGAAGAATTCAGCAGAAGAAAGATTATGTTCTTGGTTTTCCATAGTCCAC
GTGGACTATGGAAAACCAAGAACATAATCTTTCTTCTGCTGAATTCTTCAAATTTGTCTAGGTAAATGACGTTGACATATGTGAGTACTCAACTTCGTAC[A/G]
TACAAAAACTCTGTATAGTTGTTCTTGTTCTTACCATGAATGCAACACTTAAATTAATGTACTCTTCAGCAATAAAAAAAAAAGCTTATTTAACCGCTTC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 75.20% | 4.50% | 0.44% | 19.87% | NA |
| All Indica | 2759 | 63.10% | 2.60% | 0.76% | 33.53% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Aus | 269 | 49.40% | 50.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 50.90% | 0.30% | 0.67% | 48.07% | NA |
| Indica II | 465 | 71.20% | 0.00% | 0.86% | 27.96% | NA |
| Indica III | 913 | 67.50% | 3.00% | 0.22% | 29.35% | NA |
| Indica Intermediate | 786 | 62.60% | 5.30% | 1.40% | 30.66% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 3.30% | 0.00% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587475 | T -> DEL | N | N | silent_mutation | Average:62.132; most accessible tissue: Zhenshan97 young leaf, score: 76.099 | N | N | N | N |
| vg0114587475 | T -> C | LOC_Os01g25730.1 | downstream_gene_variant ; 4097.0bp to feature; MODIFIER | silent_mutation | Average:62.132; most accessible tissue: Zhenshan97 young leaf, score: 76.099 | N | N | N | N |
| vg0114587475 | T -> C | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:62.132; most accessible tissue: Zhenshan97 young leaf, score: 76.099 | N | N | N | N |