| Variant ID: vg1102344383 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 2344383 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.00, others allele: 0.00, population size: 295. )
AAGTCAAAAATCTAATTAGTTGTCTGAACTCTCAAGGATAAACAAACTTACAAGTTCATTTAGCTGCTAAAAACAAGTGATCTTAGGCATGTTATCTAGT[T/A]
AAGAGGTATTCTGCCTCAGAACCTGCAGATTTAGAAAACAAAACTATAGTCTAAATATAACAGCACTGGTTGATGCAATACCACTCGAAGGATTTCACCA
TGGTGAAATCCTTCGAGTGGTATTGCATCAACCAGTGCTGTTATATTTAGACTATAGTTTTGTTTTCTAAATCTGCAGGTTCTGAGGCAGAATACCTCTT[A/T]
ACTAGATAACATGCCTAAGATCACTTGTTTTTAGCAGCTAAATGAACTTGTAAGTTTGTTTATCCTTGAGAGTTCAGACAACTAATTAGATTTTTGACTT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 94.40% | 5.60% | 0.00% | 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 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 90.80% | 9.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1102344383 | T -> A | LOC_Os11g05280.1 | downstream_gene_variant ; 3621.0bp to feature; MODIFIER | silent_mutation | Average:65.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1102344383 | T -> A | LOC_Os11g05300.1 | downstream_gene_variant ; 1128.0bp to feature; MODIFIER | silent_mutation | Average:65.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |
| vg1102344383 | T -> A | LOC_Os11g05290.1 | intron_variant ; MODIFIER | silent_mutation | Average:65.488; most accessible tissue: Zhenshan97 panicle, score: 86.788 | N | N | N | N |