| Variant ID: vg1101693216 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1693216 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 295. )
TCAAGCAGTTCAGGGCCATGAACCAGTTCAAGAAAGCTGCACTGAGGGTAAATATTACTCTTAATCACATCATCAGGGTAGATATATGCATCTTAATTGT[T/C]
GTTTTGAATCTTCTGTAGATTATAGCCGGATGCCTGTCAGAGGAGGAGATCAAGGGGCTGAAGGAGATGTTCAAGAACATCGACAAGGACAATAGTGGGA
TCCCACTATTGTCCTTGTCGATGTTCTTGAACATCTCCTTCAGCCCCTTGATCTCCTCCTCTGACAGGCATCCGGCTATAATCTACAGAAGATTCAAAAC[A/G]
ACAATTAAGATGCATATATCTACCCTGATGATGTGATTAAGAGTAATATTTACCCTCAGTGCAGCTTTCTTGAACTGGTTCATGGCCCTGAACTGCTTGA
| 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 | 98.80% | 1.00% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.10% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.10% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 57.30% | 42.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101693216 | T -> C | LOC_Os11g04160.1 | downstream_gene_variant ; 1876.0bp to feature; MODIFIER | silent_mutation | Average:47.465; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg1101693216 | T -> C | LOC_Os11g04174.1 | downstream_gene_variant ; 1256.0bp to feature; MODIFIER | silent_mutation | Average:47.465; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg1101693216 | T -> C | LOC_Os11g04180.1 | downstream_gene_variant ; 3211.0bp to feature; MODIFIER | silent_mutation | Average:47.465; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |
| vg1101693216 | T -> C | LOC_Os11g04170.1 | intron_variant ; MODIFIER | silent_mutation | Average:47.465; most accessible tissue: Zhenshan97 panicle, score: 69.946 | N | N | N | N |