| Variant ID: vg0612160216 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160216 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGGCATAACTCTTATGTCGAGACTGAGCCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAACCTG[A/C]
CGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTGTTGT
ACAACAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACG[T/G]
CAGGTTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGGCTCAGTCTCGACATAAGAGTTATGCCG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 81.00% | 1.00% | 6.58% | 11.45% | NA |
| All Indica | 2759 | 75.50% | 1.50% | 8.52% | 14.50% | NA |
| All Japonica | 1512 | 91.90% | 0.10% | 0.79% | 7.21% | NA |
| Aus | 269 | 72.50% | 1.10% | 19.33% | 7.06% | NA |
| Indica I | 595 | 70.30% | 1.20% | 12.77% | 15.80% | NA |
| Indica II | 465 | 70.30% | 1.50% | 11.40% | 16.77% | NA |
| Indica III | 913 | 82.50% | 1.30% | 4.60% | 11.61% | NA |
| Indica Intermediate | 786 | 74.30% | 2.00% | 8.14% | 15.52% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.26% | 3.78% | NA |
| Tropical Japonica | 504 | 85.50% | 0.00% | 1.59% | 12.90% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.40% | 0.83% | 6.22% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 6.25% | 1.04% | NA |
| Intermediate | 90 | 78.90% | 1.10% | 6.67% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160216 | A -> C | LOC_Os06g21050.1 | synonymous_variant ; p.Arg1224Arg; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160216 | A -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |