| Variant ID: vg0203137684 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 3137684 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTGACAACTGGCCATAGAATTTGTTTGAAGATAGCTGTAATGTGGTTAGATTGCTGCATCTGTAGATGCTATCTAGAATTTCTCCAGTGAACTTGTTCGA[C/G]
ATAAGATCCAAAAGTTTCAGATTGGGCAGTCTGGAGAAGTTAACCTTCGAAAGCTCTCCTGTGAAGTTGTTGTGCTTGAGGTTGATGATCTTGAGACTTG
CAAGTCTCAAGATCATCAACCTCAAGCACAACAACTTCACAGGAGAGCTTTCGAAGGTTAACTTCTCCAGACTGCCCAATCTGAAACTTTTGGATCTTAT[G/C]
TCGAACAAGTTCACTGGAGAAATTCTAGATAGCATCTACAGATGCAGCAATCTAACCACATTACAGCTATCTTCAAACAAATTCTATGGCCAGTTGTCAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.00% | 0.10% | 0.21% | 1.69% | NA |
| All Indica | 2759 | 97.70% | 0.20% | 0.33% | 1.78% | NA |
| All Japonica | 1512 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 95.90% | 0.50% | 0.44% | 3.07% | NA |
| Indica Intermediate | 786 | 97.20% | 0.00% | 0.13% | 2.67% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 74.00% | 0.00% | 1.04% | 25.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0203137684 | C -> G | LOC_Os02g06280.1 | missense_variant ; p.Met94Ile; MODERATE | nonsynonymous_codon ; M94I | Average:72.473; most accessible tissue: Zhenshan97 flower, score: 88.571 | unknown | unknown | TOLERATED | 0.48 |
| vg0203137684 | C -> DEL | LOC_Os02g06280.1 | N | frameshift_variant | Average:72.473; most accessible tissue: Zhenshan97 flower, score: 88.571 | N | N | N | N |