| Variant ID: vg1105183232 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5183232 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 236. )
CCGTCCTTTCATTTTAACTCTTTTTTGGGTCTCGGTATGTTCTCTATTTTCTTACACTTTTTTCCCTCAAATCACTATCATCACGCCACATTGTATTTTC[C/A]
TTTTTTTCAGCACACTGTACCCTATATTCAGTTGCTGCCACAATTGACGCCACTCGTAGGGTAGAAGGGGCCAAGAAAGGATTGATAATCTCCACTCCAC
GTGGAGTGGAGATTATCAATCCTTTCTTGGCCCCTTCTACCCTACGAGTGGCGTCAATTGTGGCAGCAACTGAATATAGGGTACAGTGTGCTGAAAAAAA[G/T]
GAAAATACAATGTGGCGTGATGATAGTGATTTGAGGGAAAAAAGTGTAAGAAAATAGAGAACATACCGAGACCCAAAAAAGAGTTAAAATGAAAGGACGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.80% | 1.70% | 0.87% | 30.64% | NA |
| All Indica | 2759 | 48.50% | 2.50% | 1.20% | 47.77% | NA |
| All Japonica | 1512 | 98.70% | 0.10% | 0.13% | 1.12% | NA |
| Aus | 269 | 67.30% | 1.50% | 1.49% | 29.74% | NA |
| Indica I | 595 | 26.20% | 1.70% | 3.03% | 69.08% | NA |
| Indica II | 465 | 21.70% | 0.40% | 1.94% | 75.91% | NA |
| Indica III | 913 | 68.90% | 5.10% | 0.33% | 25.63% | NA |
| Indica Intermediate | 786 | 57.50% | 1.40% | 0.38% | 40.71% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.26% | 1.96% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 66.70% | 3.30% | 2.22% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183232 | C -> A | LOC_Os11g09720.1 | upstream_gene_variant ; 1490.0bp to feature; MODIFIER | silent_mutation | Average:16.484; most accessible tissue: Callus, score: 81.049 | N | N | N | N |
| vg1105183232 | C -> A | LOC_Os11g09700.1 | downstream_gene_variant ; 4222.0bp to feature; MODIFIER | silent_mutation | Average:16.484; most accessible tissue: Callus, score: 81.049 | N | N | N | N |
| vg1105183232 | C -> A | LOC_Os11g09710.1 | intron_variant ; MODIFIER | silent_mutation | Average:16.484; most accessible tissue: Callus, score: 81.049 | N | N | N | N |
| vg1105183232 | C -> DEL | N | N | silent_mutation | Average:16.484; most accessible tissue: Callus, score: 81.049 | N | N | N | N |