| Variant ID: vg0524150558 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 24150558 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.79, C: 0.21, others allele: 0.00, population size: 58. )
ATTGGTCCTTCAATATTGTTCGAAGCGATTTCCCTAACCCAAGATAGCAAAAGACAGAAAGAGTCAATAAAAACTCCATGTAACTGATGGGCTTGGCATT[A/C]
AAAAAAAAAAAACTGATGGTCTTGCAACTCTCTACAAAGAGAAGCACTAGCAAATTAAACTACATTGACATTAGTCTGCTAAATGTGCCTTTTCATTTCT
AGAAATGAAAAGGCACATTTAGCAGACTAATGTCAATGTAGTTTAATTTGCTAGTGCTTCTCTTTGTAGAGAGTTGCAAGACCATCAGTTTTTTTTTTTT[T/G]
AATGCCAAGCCCATCAGTTACATGGAGTTTTTATTGACTCTTTCTGTCTTTTGCTATCTTGGGTTAGGGAAATCGCTTCGAACAATATTGAAGGACCAAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 39.70% | 2.30% | 11.09% | 46.89% | NA |
| All Indica | 2759 | 9.60% | 3.10% | 17.07% | 70.21% | NA |
| All Japonica | 1512 | 99.30% | 0.10% | 0.07% | 0.53% | NA |
| Aus | 269 | 3.70% | 7.40% | 13.75% | 75.09% | NA |
| Indica I | 595 | 7.90% | 2.00% | 12.94% | 77.14% | NA |
| Indica II | 465 | 14.80% | 1.90% | 16.56% | 66.67% | NA |
| Indica III | 913 | 9.20% | 5.00% | 17.52% | 68.24% | NA |
| Indica Intermediate | 786 | 8.30% | 2.40% | 19.97% | 69.34% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 0.20% | 0.20% | 1.59% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 60.40% | 1.00% | 2.08% | 36.46% | NA |
| Intermediate | 90 | 45.60% | 2.20% | 14.44% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0524150558 | A -> DEL | N | N | silent_mutation | Average:72.512; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150558 | A -> C | LOC_Os05g41240.1 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.512; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150558 | A -> C | LOC_Os05g41240.3 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.512; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150558 | A -> C | LOC_Os05g41240.2 | downstream_gene_variant ; 3175.0bp to feature; MODIFIER | silent_mutation | Average:72.512; most accessible tissue: Callus, score: 93.693 | N | N | N | N |
| vg0524150558 | A -> C | LOC_Os05g41230.1 | intron_variant ; MODIFIER | silent_mutation | Average:72.512; most accessible tissue: Callus, score: 93.693 | N | N | N | N |