| Variant ID: vg0426092328 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 26092328 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 295. )
TCATCTATCATCTTGACCTTATGCCATTCACTAATAAGTCCTCATGACTTGCTAGTAAGCTACTTGGAGTGAATGTCATCAGTTGCGTGAATTCACCAAT[T/C]
ATCTTGACCTTATGACATTCACTAATTAGTCCTCATGACTTGCAATTAAGCTACTTGGAATTGGAGGTTTTATCCTGGACTACTAGTTTGGTTCCCTATG
CATAGGGAACCAAACTAGTAGTCCAGGATAAAACCTCCAATTCCAAGTAGCTTAATTGCAAGTCATGAGGACTAATTAGTGAATGTCATAAGGTCAAGAT[A/G]
ATTGGTGAATTCACGCAACTGATGACATTCACTCCAAGTAGCTTACTAGCAAGTCATGAGGACTTATTAGTGAATGGCATAAGGTCAAGATGATAGATGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426092328 | T -> C | LOC_Os04g44030.1 | 3_prime_UTR_variant ; 191.0bp to feature; MODIFIER | N | Average:57.976; most accessible tissue: Minghui63 flower, score: 72.046 | N | N | N | N |
| vg0426092328 | T -> C | LOC_Os04g44020.1 | downstream_gene_variant ; 4544.0bp to feature; MODIFIER | N | Average:57.976; most accessible tissue: Minghui63 flower, score: 72.046 | N | N | N | N |