| Variant ID: vg0612160252 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160252 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCG[G/A]
CACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTGTTGTATGAAAATTCTGCATAAGGTAGATTCTTATCCCAAC
GTTGGGATAAGAATCTACCTTATGCAGAATTTTCATACAACAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTG[C/T]
CGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 32.50% | 0.90% | 20.55% | 46.11% | NA |
| All Indica | 2759 | 4.90% | 1.40% | 22.54% | 71.11% | NA |
| All Japonica | 1512 | 88.20% | 0.10% | 3.04% | 8.73% | NA |
| Aus | 269 | 8.90% | 0.00% | 76.58% | 14.50% | NA |
| Indica I | 595 | 8.90% | 1.30% | 10.25% | 79.50% | NA |
| Indica II | 465 | 5.20% | 1.10% | 12.69% | 81.08% | NA |
| Indica III | 913 | 1.50% | 0.90% | 36.91% | 60.68% | NA |
| Indica Intermediate | 786 | 5.70% | 2.30% | 20.99% | 70.99% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 1.17% | 1.69% | NA |
| Tropical Japonica | 504 | 73.40% | 0.00% | 6.75% | 19.84% | NA |
| Japonica Intermediate | 241 | 90.50% | 0.40% | 1.24% | 7.88% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 82.29% | 10.42% | NA |
| Intermediate | 90 | 38.90% | 1.10% | 20.00% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160252 | G -> A | LOC_Os06g21050.1 | synonymous_variant ; p.Cys1212Cys; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160252 | G -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |