| Variant ID: vg0612160228 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160228 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TATGTCGAGACTGAGCCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAACCTGACGTTCTCCCGT[T/C]
TGATCCCACAAAAGCGGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTGTTGTATGAAAATTCTG
CAGAATTTTCATACAACAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCCGCTTTTGTGGGATCA[A/G]
ACGGGAGAACGTCAGGTTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGGCTCAGTCTCGACATA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.20% | 0.10% | 5.25% | 10.47% | NA |
| All Indica | 2759 | 80.20% | 0.20% | 6.63% | 12.94% | NA |
| All Japonica | 1512 | 92.20% | 0.00% | 0.79% | 7.01% | NA |
| Aus | 269 | 75.80% | 0.00% | 17.10% | 7.06% | NA |
| Indica I | 595 | 76.10% | 0.20% | 10.08% | 13.61% | NA |
| Indica II | 465 | 76.10% | 0.00% | 9.68% | 14.19% | NA |
| Indica III | 913 | 85.50% | 0.50% | 3.18% | 10.73% | NA |
| Indica Intermediate | 786 | 79.50% | 0.00% | 6.23% | 14.25% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.26% | 3.78% | NA |
| Tropical Japonica | 504 | 85.90% | 0.00% | 1.79% | 12.30% | 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 | 85.60% | 0.00% | 1.11% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160228 | T -> C | LOC_Os06g21050.1 | synonymous_variant ; p.Gln1220Gln; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160228 | T -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |