| Variant ID: vg0612160189 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12160189 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAAAACTCAAATCTCTACGGCGATTGTCGGCATAACTCTTATGTCGAGACTGAGCCACTCGCAATCTTTATTGAATGATCTTTACCTTTTCTTCTGCTTC[C/T]
CTTAGGATATCCGTCCCAAAAACCTGACGTTCTCCCGTTTGATCCCACAAAAGCGGAGTGCGGCACTTTCGACCATACAGTGCTTCGTAAGGAGCCATCT
AGATGGCTCCTTACGAAGCACTGTATGGTCGAAAGTGCCGCACTCCGCTTTTGTGGGATCAAACGGGAGAACGTCAGGTTTTTGGGACGGATATCCTAAG[G/A]
GAAGCAGAAGAAAAGGTAAAGATCATTCAATAAAGATTGCGAGTGGCTCAGTCTCGACATAAGAGTTATGCCGACAATCGCCGTAGAGATTTGAGTTTTG
| 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% | 0.10% | 5.40% | 11.21% | NA |
| All Indica | 2759 | 79.20% | 0.10% | 6.52% | 14.21% | NA |
| All Japonica | 1512 | 92.10% | 0.00% | 0.86% | 7.01% | NA |
| Aus | 269 | 72.50% | 0.70% | 19.70% | 7.06% | NA |
| Indica I | 595 | 73.90% | 0.00% | 10.42% | 15.63% | NA |
| Indica II | 465 | 75.10% | 0.20% | 8.39% | 16.34% | NA |
| Indica III | 913 | 85.70% | 0.10% | 2.85% | 11.39% | NA |
| Indica Intermediate | 786 | 78.10% | 0.00% | 6.74% | 15.14% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.52% | 3.52% | NA |
| Tropical Japonica | 504 | 85.70% | 0.00% | 1.59% | 12.70% | 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 | 83.30% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0612160189 | C -> T | LOC_Os06g21050.1 | synonymous_variant ; p.Arg1233Arg; LOW | synonymous_codon | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |
| vg0612160189 | C -> DEL | LOC_Os06g21050.1 | N | frameshift_variant | Average:4.878; most accessible tissue: Callus, score: 8.991 | N | N | N | N |