| Variant ID: vg1109585099 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9585099 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 400. )
TTCTGCTTCTTGAAGTTGGTGGTCTGCTGAGCTTTGTATTTCCCCTTGCTCTTGTTCTGGGCCTTGTGCACAACATTGGCACTGGACTGCCCACCATCGC[C/T]
CTTAGACGCGACATCTTTTTCCCGAGCTTTCTCCTCAACATCAAGAGACGCTATCAACCCCTCAACGGAGTATTCCTGTCTCTTGTGTTTGAGTGCAGTA
TACTGCACTCAAACACAAGAGACAGGAATACTCCGTTGAGGGGTTGATAGCGTCTCTTGATGTTGAGGAGAAAGCTCGGGAAAAAGATGTCGCGTCTAAG[G/A]
GCGATGGTGGGCAGTCCAGTGCCAATGTTGTGCACAAGGCCCAGAACAAGAGCAAGGGGAAATACAAAGCTCAGCAGACCACCAACTTCAAGAAGCAGAA
| 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 | 78.60% | 0.00% | 3.30% | 18.09% | NA |
| All Indica | 2759 | 96.00% | 0.00% | 2.68% | 1.34% | NA |
| All Japonica | 1512 | 45.60% | 0.00% | 1.46% | 52.91% | NA |
| Aus | 269 | 78.80% | 0.00% | 20.07% | 1.12% | NA |
| Indica I | 595 | 94.50% | 0.00% | 2.18% | 3.36% | NA |
| Indica II | 465 | 96.10% | 0.00% | 3.01% | 0.86% | NA |
| Indica III | 913 | 99.70% | 0.00% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 92.70% | 0.00% | 5.73% | 1.53% | NA |
| Temperate Japonica | 767 | 26.30% | 0.00% | 1.69% | 71.97% | NA |
| Tropical Japonica | 504 | 69.80% | 0.00% | 1.19% | 28.97% | NA |
| Japonica Intermediate | 241 | 56.40% | 0.00% | 1.24% | 42.32% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 3.12% | 6.25% | NA |
| Intermediate | 90 | 86.70% | 0.00% | 3.33% | 10.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109585099 | C -> T | LOC_Os11g17200.1 | missense_variant ; p.Gly196Ser; MODERATE | N | Average:8.049; most accessible tissue: Zhenshan97 flag leaf, score: 16.47 | N | N | N | N |