| Variant ID: vg0101948741 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 1948741 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )
CTTATCACATTCCATTTCTTCGGCTGAAGTTTCAAATCAGACCACCGCACACCTAGGAGTATAACTGTTGTCAAAAGCTAGTATAACACAGTATATATAA[C/T]
ATCGGAATTCAAAAACGTTTGCATGATGTTTGCAACCTGAAAAGCTCTTTATTTATTCCTCAACGAGCAAGAACTAAGAAGGCGATTACACAAGTACTCA
TGAGTACTTGTGTAATCGCCTTCTTAGTTCTTGCTCGTTGAGGAATAAATAAAGAGCTTTTCAGGTTGCAAACATCATGCAAACGTTTTTGAATTCCGAT[G/A]
TTATATATACTGTGTTATACTAGCTTTTGACAACAGTTATACTCCTAGGTGTGCGGTGGTCTGATTTGAAACTTCAGCCGAAGAAATGGAATGTGATAAG
| 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 | 96.00% | 4.00% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 75.50% | 24.50% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 92.40% | 7.60% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 68.80% | 31.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0101948741 | C -> T | LOC_Os01g04370.1 | 3_prime_UTR_variant ; 264.0bp to feature; MODIFIER | silent_mutation | Average:63.981; most accessible tissue: Callus, score: 80.008 | N | N | N | N |
| vg0101948741 | C -> T | LOC_Os01g04360.1 | upstream_gene_variant ; 3706.0bp to feature; MODIFIER | silent_mutation | Average:63.981; most accessible tissue: Callus, score: 80.008 | N | N | N | N |
| vg0101948741 | C -> T | LOC_Os01g04380.1 | upstream_gene_variant ; 3187.0bp to feature; MODIFIER | silent_mutation | Average:63.981; most accessible tissue: Callus, score: 80.008 | N | N | N | N |