| Variant ID: vg0629027203 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29027203 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.53, T: 0.47, others allele: 0.00, population size: 104. )
GCCATCTATCGCCCAATTGCCCTCCAAGAACATGCAACCTGCACAAGTGCAGAGGCCTGCATCCCCCTCGAGGTAGATCACGTCACGTCGCACGTGTGCA[A/T]
CGCATCGTGTGCCATGTCATCAGTTGGGGAACCTGCAGTCGCGGCGGATCTCGCCGCCGGTGGCCGGCGACTTGACGCCGACCCTGCCGAGCTTGGTCAT
ATGACCAAGCTCGGCAGGGTCGGCGTCAAGTCGCCGGCCACCGGCGGCGAGATCCGCCGCGACTGCAGGTTCCCCAACTGATGACATGGCACACGATGCG[T/A]
TGCACACGTGCGACGTGACGTGATCTACCTCGAGGGGGATGCAGGCCTCTGCACTTGTGCAGGTTGCATGTTCTTGGAGGGCAATTGGGCGATAGATGGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 52.60% | 47.10% | 0.30% | 0.00% | NA |
| All Indica | 2759 | 78.40% | 21.10% | 0.47% | 0.00% | NA |
| All Japonica | 1512 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 45.00% | 55.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 86.20% | 13.40% | 0.34% | 0.00% | NA |
| Indica II | 465 | 88.60% | 11.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 72.60% | 26.60% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 73.30% | 26.30% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 2.70% | 97.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 4.10% | 95.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 55.60% | 43.30% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027203 | A -> T | LOC_Os06g48010.1 | 3_prime_UTR_variant ; 20.0bp to feature; MODIFIER | silent_mutation | Average:69.894; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0629027203 | A -> T | LOC_Os06g48000.1 | downstream_gene_variant ; 3711.0bp to feature; MODIFIER | silent_mutation | Average:69.894; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |