| Variant ID: vg0612160237 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160237 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACTGAGCCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTCCCTTAGGATATCCGTCCCAAAAACCTGACGTTCTCCCGTTTGATCCCA[C/T]
AAAAGCGGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCTGTAAACTAGTTTGATAACTGTTGTTGTATGAAAATTCTGCATAAGGTA
TACCTTATGCAGAATTTTCATACAACAACAGTTATCAAACTAGTTTACAGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCCGCTTTT[G/A]
TGGGATCAAACGGGAGAACGTCAGGTTTTTGGGACGGATATCCTAAGGGAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGGCTCAGT
| 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 | 80.40% | 0.10% | 4.87% | 14.60% | NA |
| All Indica | 2759 | 74.80% | 0.20% | 7.54% | 17.47% | NA |
| All Japonica | 1512 | 91.60% | 0.00% | 0.86% | 7.54% | NA |
| Aus | 269 | 73.20% | 0.40% | 1.12% | 25.28% | NA |
| Indica I | 595 | 69.90% | 0.30% | 9.41% | 20.34% | NA |
| Indica II | 465 | 70.10% | 0.00% | 9.25% | 20.65% | NA |
| Indica III | 913 | 82.50% | 0.10% | 5.04% | 12.38% | NA |
| Indica Intermediate | 786 | 72.30% | 0.40% | 8.02% | 19.34% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.00% | 4.04% | NA |
| Tropical Japonica | 504 | 84.50% | 0.00% | 1.98% | 13.49% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.00% | 1.24% | 6.22% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 3.12% | 10.42% | NA |
| Intermediate | 90 | 78.90% | 0.00% | 3.33% | 17.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160237 | C -> T | LOC_Os06g21050.1 | synonymous_variant ; p.Leu1217Leu; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160237 | C -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |