| Variant ID: vg1126363963 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26363963 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCTTCCTGCGGGCAAACGCTGACGTCTTCGCATGGAGACCAGCGGACATGCCCGGGGTCCCCAGGGAGGTGATTGAGCACCGTCTCGCCGTGCGGCCGGG[C/T]
GCAAGGCCGGTCCGGCAGAAAGTGCGGCGGCAGGCCCCGGAACGTCAAGCCTTCATCCGCGAGGAGGTGGCGAGACTTCTGGAGGCCGGATTCATCCGTG
CACGGATGAATCCGGCCTCCAGAAGTCTCGCCACCTCCTCGCGGATGAAGGCTTGACGTTCCGGGGCCTGCCGCCGCACTTTCTGCCGGACCGGCCTTGC[G/A]
CCCGGCCGCACGGCGAGACGGTGCTCAATCACCTCCCTGGGGACCCCGGGCATGTCCGCTGGTCTCCATGCGAAGACGTCAGCGTTTGCCCGCAGGAAGG
| 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 | 0.30% | 0.10% | 21.82% | 77.78% | NA |
| All Indica | 2759 | 0.00% | 0.20% | 9.13% | 90.69% | NA |
| All Japonica | 1512 | 0.80% | 0.10% | 42.39% | 56.68% | NA |
| Aus | 269 | 0.00% | 0.00% | 27.88% | 72.12% | NA |
| Indica I | 595 | 0.00% | 0.00% | 5.71% | 94.29% | NA |
| Indica II | 465 | 0.00% | 0.20% | 3.66% | 96.13% | NA |
| Indica III | 913 | 0.00% | 0.30% | 14.68% | 84.99% | NA |
| Indica Intermediate | 786 | 0.00% | 0.10% | 8.52% | 91.35% | NA |
| Temperate Japonica | 767 | 0.10% | 0.30% | 34.42% | 65.19% | NA |
| Tropical Japonica | 504 | 0.60% | 0.00% | 52.18% | 47.22% | NA |
| Japonica Intermediate | 241 | 3.30% | 0.00% | 47.30% | 49.38% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 44.79% | 55.21% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 22.22% | 77.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126363963 | C -> T | LOC_Os11g43670.1 | synonymous_variant ; p.Gly824Gly; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1126363963 | C -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |