| Variant ID: vg0702311882 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 2311882 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 128. )
GCCAGCACACGGCGAACCTGATCAAAGGCAAGTCGCCGGAGCAGATCAGGAAGGAGTTTGGGATCAAGAACGACTTCACGCCGGAGGAGGAGGAGGAAAT[C/T]
CGCAAGGAGAACACATGGGCCTTCGAGTAGATTTTCCTTTGGGAAAATATTTATGCTAATTAATTATGTCATGTTGCTGCGAATTACTGCTCTAATTAGT
ACTAATTAGAGCAGTAATTCGCAGCAACATGACATAATTAATTAGCATAAATATTTTCCCAAAGGAAAATCTACTCGAAGGCCCATGTGTTCTCCTTGCG[G/A]
ATTTCCTCCTCCTCCTCCGGCGTGAAGTCGTTCTTGATCCCAAACTCCTTCCTGATCTGCTCCGGCGACTTGCCTTTGATCAGGTTCGCCGTGTGCTGGC
| 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 | 94.70% | 4.30% | 0.93% | 0.00% | NA |
| All Indica | 2759 | 91.30% | 7.10% | 1.56% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.60% | 0.50% | 1.85% | 0.00% | NA |
| Indica II | 465 | 77.40% | 18.50% | 4.09% | 0.00% | NA |
| Indica III | 913 | 97.60% | 2.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 87.50% | 10.90% | 1.53% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 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 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0702311882 | C -> T | LOC_Os07g05180.1 | synonymous_variant ; p.Ile155Ile; LOW | synonymous_codon | Average:63.501; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |