| Variant ID: vg0629027109 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29027109 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 291. )
ACTTATTCGGATCGTTGACAAAAACAACTTAAATTTTTGAACACACAATAATGTACTACCGATTGTTTTTTCCCCAAATCCAAAAGGAAAGATTGCCATC[T/C]
ATCGCCCAATTGCCCTCCAAGAACATGCAACCTGCACAAGTGCAGAGGCCTGCATCCCCCTCGAGGTAGATCACGTCACGTCGCACGTGTGCAACGCATC
GATGCGTTGCACACGTGCGACGTGACGTGATCTACCTCGAGGGGGATGCAGGCCTCTGCACTTGTGCAGGTTGCATGTTCTTGGAGGGCAATTGGGCGAT[A/G]
GATGGCAATCTTTCCTTTTGGATTTGGGGAAAAAACAATCGGTAGTACATTATTGTGTGTTCAAAAATTTAAGTTGTTTTTGTCAACGATCCGAATAAGT
| 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 | 90.00% | 9.70% | 0.32% | 0.00% | NA |
| All Indica | 2759 | 83.30% | 16.20% | 0.54% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.80% | 3.90% | 0.34% | 0.00% | NA |
| Indica II | 465 | 91.80% | 8.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 74.80% | 24.80% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 78.50% | 20.50% | 1.02% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027109 | T -> C | LOC_Os06g48010.1 | 3_prime_UTR_variant ; 114.0bp to feature; MODIFIER | silent_mutation | Average:62.16; most accessible tissue: Minghui63 root, score: 77.565 | N | N | N | N |
| vg0629027109 | T -> C | LOC_Os06g48000.1 | downstream_gene_variant ; 3617.0bp to feature; MODIFIER | silent_mutation | Average:62.16; most accessible tissue: Minghui63 root, score: 77.565 | N | N | N | N |