| Variant ID: vg0410079496 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079496 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
GGGAGGACGACCTAGGGGTGCCTAGGGTCGTGCTCCACCTGGCTGGGGCGCACCCCACATGGGCCCCACCTGGGCCGGGGTCCCAGACGAAGTTACAAGC[C/T]
CATAGGCCCATTATAGGTGACGCAGCACCTTGTTGCTTCAATTGCGGCTCAATAAGATGGAATTTCGCAATGAGGCTGGATCCATTGGAAAGAGGACTCC
GGAGTCCTCTTTCCAATGGATCCAGCCTCATTGCGAAATTCCATCTTATTGAGCCGCAATTGAAGCAACAAGGTGCTGCGTCACCTATAATGGGCCTATG[G/A]
GCTTGTAACTTCGTCTGGGACCCCGGCCCAGGTGGGGCCCATGTGGGGTGCGCCCCAGCCAGGTGGAGCACGACCCTAGGCACCCCTAGGTCGTCCTCCC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.60% | 0.00% | 6.69% | 72.70% | NA |
| All Indica | 2759 | 1.10% | 0.00% | 7.03% | 91.84% | NA |
| All Japonica | 1512 | 61.00% | 0.00% | 3.04% | 35.91% | NA |
| Aus | 269 | 0.00% | 0.00% | 9.29% | 90.71% | NA |
| Indica I | 595 | 1.30% | 0.00% | 6.89% | 91.76% | NA |
| Indica II | 465 | 1.50% | 0.00% | 5.59% | 92.90% | NA |
| Indica III | 913 | 0.80% | 0.00% | 7.01% | 92.22% | NA |
| Indica Intermediate | 786 | 1.10% | 0.00% | 8.02% | 90.84% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.26% | 3.91% | NA |
| Tropical Japonica | 504 | 4.80% | 0.00% | 8.13% | 87.10% | NA |
| Japonica Intermediate | 241 | 68.00% | 0.00% | 1.24% | 30.71% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 38.54% | 60.42% | NA |
| Intermediate | 90 | 21.10% | 0.00% | 15.56% | 63.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079496 | C -> T | LOC_Os04g18230.1 | stop_gained ; p.Trp93*; HIGH | N | Average:4.479; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |