| Variant ID: vg0905621475 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5621475 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 222. )
GATCACTAGTCAACGTCATGCGAACACGACTATTCTCCTCATTGGGGTCATGGGGAATTTGGCGATACTCGGGGACAATGTTGTAGCCTACTTCAAATGC[C/T]
ATCATTCTCAGCTCCCTGACGAATCCTACTGCATCGATCAAGCTTTCTGGCATCTAAAGGAACACATAAAGGAGGAATTAATGCATATATTTAAGTTAGC
GCTAACTTAAATATATGCATTAATTCCTCCTTTATGTGTTCCTTTAGATGCCAGAAAGCTTGATCGATGCAGTAGGATTCGTCAGGGAGCTGAGAATGAT[G/A]
GCATTTGAAGTAGGCTACAACATTGTCCCCGAGTATCGCCAAATTCCCCATGACCCCAATGAGGAGAATAGTCGTGTTCGCATGACGTTGACTAGTGATC
| 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 | 53.60% | 46.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 88.00% | 12.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 18.20% | 81.80% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.10% | 7.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 85.40% | 14.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 83.00% | 17.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 44.40% | 55.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0905621475 | C -> T | LOC_Os09g10310.1 | missense_variant ; p.Met18Ile; MODERATE | nonsynonymous_codon ; M18I | Average:36.062; most accessible tissue: Callus, score: 57.912 | unknown | unknown | DELETERIOUS | 0.00 |