| Variant ID: vg0612160204 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160204 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TACGGCGATTGTCGGCATAACTCTTATGTCGAGACTGAGCCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGT[C/T]
CCAAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGAT
ATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTTGG[G/A]
ACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGGCTCAGTCTCGACATAAGAGTTATGCCGACAATCGCCGTA
| 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 | 83.30% | 0.20% | 5.01% | 11.51% | NA |
| All Indica | 2759 | 79.10% | 0.30% | 6.09% | 14.46% | NA |
| All Japonica | 1512 | 91.90% | 0.00% | 0.60% | 7.47% | NA |
| Aus | 269 | 74.00% | 0.00% | 18.96% | 7.06% | NA |
| Indica I | 595 | 75.10% | 0.00% | 9.08% | 15.80% | NA |
| Indica II | 465 | 75.50% | 0.00% | 8.60% | 15.91% | NA |
| Indica III | 913 | 84.60% | 0.80% | 2.74% | 11.94% | NA |
| Indica Intermediate | 786 | 78.00% | 0.30% | 6.23% | 15.52% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.26% | 3.78% | NA |
| Tropical Japonica | 504 | 85.10% | 0.00% | 1.19% | 13.69% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.00% | 0.41% | 6.22% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 6.25% | 1.04% | NA |
| Intermediate | 90 | 82.20% | 1.10% | 3.33% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160204 | C -> T | LOC_Os06g21050.1 | synonymous_variant ; p.Gly1228Gly; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160204 | C -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |