| Variant ID: vg1117780482 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17780482 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 313. )
TTTACTCTTCGACCTGGAGGCCTGCACCGTCAACGTATATGACTCAATGGATAAAAAAGAGTCTACGTTTGACAAGGTTTTCGAACTTATAGACAGGTAC[C/T]
GTCATAAGTTCCTTTGTTAATTAAGAAAATCTTGTTATGTTAATTGCTACTACGAATCATAGCTTTAAACTCTATGTAGGGCTTGGTATCGGTTCCGTCA
TGACGGAACCGATACCAAGCCCTACATAGAGTTTAAAGCTATGATTCGTAGTAGCAATTAACATAACAAGATTTTCTTAATTAACAAAGGAACTTATGAC[G/A]
GTACCTGTCTATAAGTTCGAAAACCTTGTCAAACGTAGACTCTTTTTTATCCATTGAGTCATATACGTTGACGGTGCAGGCCTCCAGGTCGAAGAGTAAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.80% | 0.30% | 0.53% | 74.38% | NA |
| All Indica | 2759 | 7.60% | 0.50% | 0.14% | 91.70% | NA |
| All Japonica | 1512 | 54.30% | 0.00% | 0.86% | 44.84% | NA |
| Aus | 269 | 9.70% | 0.00% | 1.12% | 89.22% | NA |
| Indica I | 595 | 6.40% | 0.00% | 0.17% | 93.45% | NA |
| Indica II | 465 | 22.20% | 0.00% | 0.22% | 77.63% | NA |
| Indica III | 913 | 1.50% | 1.10% | 0.11% | 97.26% | NA |
| Indica Intermediate | 786 | 7.00% | 0.60% | 0.13% | 92.24% | NA |
| Temperate Japonica | 767 | 63.10% | 0.00% | 1.69% | 35.20% | NA |
| Tropical Japonica | 504 | 28.00% | 0.00% | 0.00% | 72.02% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 0.00% | 18.67% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 28.90% | 1.10% | 4.44% | 65.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117780482 | C -> T | LOC_Os11g30552.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1117780482 | C -> T | LOC_Os11g30560.1 | upstream_gene_variant ; 4656.0bp to feature; MODIFIER | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg1117780482 | C -> DEL | N | N | silent_mutation | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |