| Variant ID: vg0612160243 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160243 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAG[C/T,A]
GGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTGTTGTATGAAAATTCTGCATAAGGTAGATTCT
AGAATCTACCTTATGCAGAATTTTCATACAACAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCC[G/A,T]
CTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.80% | 0.30% | 22.98% | 30.70% | T: 0.23% |
| All Indica | 2759 | 21.00% | 0.50% | 34.72% | 43.42% | T: 0.40% |
| All Japonica | 1512 | 89.50% | 0.00% | 1.98% | 8.53% | NA |
| Aus | 269 | 41.30% | 0.00% | 29.00% | 29.74% | NA |
| Indica I | 595 | 20.20% | 0.20% | 24.37% | 54.96% | T: 0.34% |
| Indica II | 465 | 18.70% | 0.20% | 31.40% | 49.25% | T: 0.43% |
| Indica III | 913 | 21.10% | 0.40% | 46.88% | 31.43% | T: 0.11% |
| Indica Intermediate | 786 | 22.80% | 0.90% | 30.41% | 45.17% | T: 0.76% |
| Temperate Japonica | 767 | 95.40% | 0.00% | 0.26% | 4.30% | NA |
| Tropical Japonica | 504 | 79.00% | 0.00% | 5.56% | 15.48% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 0.00% | 7.47% | NA |
| VI/Aromatic | 96 | 75.00% | 1.00% | 7.29% | 16.67% | NA |
| Intermediate | 90 | 54.40% | 0.00% | 14.44% | 31.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160243 | C -> T | LOC_Os06g21050.1 | synonymous_variant ; p.Pro1215Pro; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160243 | C -> A | LOC_Os06g21050.1 | synonymous_variant ; p.Pro1215Pro; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160243 | C -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |