| Variant ID: vg1126903435 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903435 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 35. )
AGGCTGGACGACGAGTGATGTCCATGTGGCTGATAACGGGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTTTTCAGCCTGCCT[C/T]
CCGGCCATCACCAACCTGTACATGGCGCTATTGTCCTGGCATGCCATCACAAGCTCGTGCGCCTCCCGGAGCGTGTCGTCGAGCCCGGTGAAGACGCGGC
GCCGCGTCTTCACCGGGCTCGACGACACGCTCCGGGAGGCGCACGAGCTTGTGATGGCATGCCAGGACAATAGCGCCATGTACAGGTTGGTGATGGCCGG[G/A]
AGGCAGGCTGAAAAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCCCGTTATCAGCCACATGGACATCACTCGTCGTCCAGCCT
| 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 | 42.10% | 18.70% | 5.50% | 33.71% | NA |
| All Indica | 2759 | 42.80% | 10.00% | 4.89% | 42.26% | NA |
| All Japonica | 1512 | 37.00% | 36.80% | 5.16% | 21.10% | NA |
| Aus | 269 | 50.90% | 13.40% | 13.38% | 22.30% | NA |
| Indica I | 595 | 31.10% | 17.60% | 2.69% | 48.57% | NA |
| Indica II | 465 | 60.40% | 4.30% | 1.29% | 33.98% | NA |
| Indica III | 913 | 42.80% | 3.20% | 8.21% | 45.78% | NA |
| Indica Intermediate | 786 | 41.20% | 15.60% | 4.83% | 38.30% | NA |
| Temperate Japonica | 767 | 17.90% | 63.90% | 2.61% | 15.65% | NA |
| Tropical Japonica | 504 | 60.70% | 3.00% | 9.33% | 26.98% | NA |
| Japonica Intermediate | 241 | 48.10% | 21.20% | 4.56% | 26.14% | NA |
| VI/Aromatic | 96 | 81.20% | 0.00% | 3.12% | 15.62% | NA |
| Intermediate | 90 | 40.00% | 14.40% | 8.89% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903435 | C -> T | LOC_Os11g44460.1 | synonymous_variant ; p.Gly80Gly; LOW | synonymous_codon | Average:16.004; most accessible tissue: Callus, score: 62.316 | N | N | N | N |
| vg1126903435 | C -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:16.004; most accessible tissue: Callus, score: 62.316 | N | N | N | N |