| Variant ID: vg0203136530 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 3136530 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 268. )
ACACAGAAGAATGCGACAAAAGCAATCGCAAAGATGGTCTTTTGAGTGCTTTGTTCTCTGGAGTCTGAAAACTGGAGGTGTTTTTGCCGATGCACAGGTG[C/T]
GAATGAGCGTATGACCACACAGCTTTGGGTTCCCATCAAAACCCCAATACTCATATCCAATTGGAACTGACCCCTCTAAGTCGTTGTTAGAAACATCAAA
TTTGATGTTTCTAACAACGACTTAGAGGGGTCAGTTCCAATTGGATATGAGTATTGGGGTTTTGATGGGAACCCAAAGCTGTGTGGTCATACGCTCATTC[G/A]
CACCTGTGCATCGGCAAAAACACCTCCAGTTTTCAGACTCCAGAGAACAAAGCACTCAAAAGACCATCTTTGCGATTGCTTTTGTCGCATTCTTCTGTGT
| 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 | 97.80% | 0.20% | 0.21% | 1.80% | NA |
| All Indica | 2759 | 97.80% | 0.00% | 0.25% | 1.96% | NA |
| All Japonica | 1512 | 99.10% | 0.60% | 0.07% | 0.20% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | 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 | 96.40% | 0.00% | 0.33% | 3.29% | NA |
| Indica Intermediate | 786 | 96.40% | 0.00% | 0.51% | 3.05% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 1.80% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 2.08% | 25.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0203136530 | C -> T | LOC_Os02g06270.1 | upstream_gene_variant ; 1545.0bp to feature; MODIFIER | silent_mutation | Average:54.504; most accessible tissue: Callus, score: 86.347 | N | N | N | N |
| vg0203136530 | C -> T | LOC_Os02g06280.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.504; most accessible tissue: Callus, score: 86.347 | N | N | N | N |
| vg0203136530 | C -> DEL | N | N | silent_mutation | Average:54.504; most accessible tissue: Callus, score: 86.347 | N | N | N | N |