| Variant ID: vg0426638515 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 26638515 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.06, others allele: 0.00, population size: 259. )
TGCTGGAGCGCCGTCCCCGTGAAGGCCGGTAAGACCACGGTTCCGAGCTCCGCCTGCGACGATTTCGCCGGGGAATTCACCGCGAATTTTGCAACTGCTG[T/C]
ACGCCTGAATGCATTGCACCTGTGTCCTGCTTCAAAACCCCCCTGTTTGCTTGTTGCTGCTCTCGTTTTTTTCTTTTTTTTTTCAAATGCACCTTGATTT
AAATCAAGGTGCATTTGAAAAAAAAAAGAAAAAAACGAGAGCAGCAACAAGCAAACAGGGGGGTTTTGAAGCAGGACACAGGTGCAATGCATTCAGGCGT[A/G]
CAGCAGTTGCAAAATTCGCGGTGAATTCCCCGGCGAAATCGTCGCAGGCGGAGCTCGGAACCGTGGTCTTACCGGCCTTCACGGGGACGGCGCTCCAGCA
| 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 | 95.50% | 4.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 54.30% | 45.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426638515 | T -> C | LOC_Os04g45030.1 | downstream_gene_variant ; 3656.0bp to feature; MODIFIER | silent_mutation | Average:68.535; most accessible tissue: Callus, score: 91.835 | N | N | N | N |
| vg0426638515 | T -> C | LOC_Os04g45020.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.535; most accessible tissue: Callus, score: 91.835 | N | N | N | N |