| Variant ID: vg1101693689 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1693689 |
| Reference Allele: G | Alternative Allele: T,C |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 286. )
CGGCATTCCAGTACTTTGACAAGGATAATAGTGGGTAAGTTAAGGATAGCAAAAACTGATATAACTGAATTCTGAACTTCAGGGATTTGTACACATTTAT[G/T,C]
CCATCCCTCTTGCAGGTACATCACAAAGGAAGAGCTCGAGCAAGCCTTGAAGGAACAAGGGTTATACGACGCCAACGAGATCAAGGATGTCATCACAGAT
ATCTGTGATGACATCCTTGATCTCGTTGGCGTCGTATAACCCTTGTTCCTTCAAGGCTTGCTCGAGCTCTTCCTTTGTGATGTACCTGCAAGAGGGATGG[C/A,G]
ATAAATGTGTACAAATCCCTGAAGTTCAGAATTCAGTTATATCAGTTTTTGCTATCCTTAACTTACCCACTATTATCCTTGTCAAAGTACTGGAATGCCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.00% | 0.40% | 8.06% | 57.43% | C: 0.06% |
| All Indica | 2759 | 2.60% | 0.70% | 8.34% | 88.40% | C: 0.04% |
| All Japonica | 1512 | 96.00% | 0.00% | 0.93% | 3.04% | NA |
| Aus | 269 | 1.50% | 0.00% | 29.00% | 69.52% | NA |
| Indica I | 595 | 1.30% | 2.00% | 6.55% | 90.08% | NA |
| Indica II | 465 | 3.00% | 0.20% | 4.30% | 92.47% | NA |
| Indica III | 913 | 1.60% | 0.00% | 9.53% | 88.83% | NA |
| Indica Intermediate | 786 | 4.30% | 0.60% | 10.69% | 84.22% | C: 0.13% |
| Temperate Japonica | 767 | 97.00% | 0.00% | 0.13% | 2.87% | NA |
| Tropical Japonica | 504 | 95.20% | 0.00% | 0.99% | 3.77% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 3.32% | 2.07% | NA |
| VI/Aromatic | 96 | 39.60% | 0.00% | 52.08% | 8.33% | NA |
| Intermediate | 90 | 48.90% | 1.10% | 10.00% | 37.78% | C: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101693689 | G -> T | LOC_Os11g04160.1 | downstream_gene_variant ; 2349.0bp to feature; MODIFIER | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1101693689 | G -> T | LOC_Os11g04174.1 | downstream_gene_variant ; 783.0bp to feature; MODIFIER | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1101693689 | G -> T | LOC_Os11g04180.1 | downstream_gene_variant ; 2738.0bp to feature; MODIFIER | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1101693689 | G -> T | LOC_Os11g04170.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1101693689 | G -> DEL | N | N | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1101693689 | G -> C | LOC_Os11g04160.1 | downstream_gene_variant ; 2349.0bp to feature; MODIFIER | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1101693689 | G -> C | LOC_Os11g04174.1 | downstream_gene_variant ; 783.0bp to feature; MODIFIER | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1101693689 | G -> C | LOC_Os11g04180.1 | downstream_gene_variant ; 2738.0bp to feature; MODIFIER | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |
| vg1101693689 | G -> C | LOC_Os11g04170.1 | intron_variant ; MODIFIER | silent_mutation | Average:30.447; most accessible tissue: Zhenshan97 panicle, score: 52.263 | N | N | N | N |