| Variant ID: vg0629027213 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29027213 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.61, C: 0.39, others allele: 0.00, population size: 97. )
GCCCAATTGCCCTCCAAGAACATGCAACCTGCACAAGTGCAGAGGCCTGCATCCCCCTCGAGGTAGATCACGTCACGTCGCACGTGTGCAACGCATCGTG[T/C]
GCCATGTCATCAGTTGGGGAACCTGCAGTCGCGGCGGATCTCGCCGCCGGTGGCCGGCGACTTGACGCCGACCCTGCCGAGCTTGGTCATGGCGGCGACG
CGTCGCCGCCATGACCAAGCTCGGCAGGGTCGGCGTCAAGTCGCCGGCCACCGGCGGCGAGATCCGCCGCGACTGCAGGTTCCCCAACTGATGACATGGC[A/G]
CACGATGCGTTGCACACGTGCGACGTGACGTGATCTACCTCGAGGGGGATGCAGGCCTCTGCACTTGTGCAGGTTGCATGTTCTTGGAGGGCAATTGGGC
| 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 | 50.70% | 47.50% | 1.33% | 0.53% | NA |
| All Indica | 2759 | 75.40% | 21.70% | 2.10% | 0.80% | NA |
| All Japonica | 1512 | 4.00% | 95.90% | 0.07% | 0.07% | NA |
| Aus | 269 | 43.90% | 55.00% | 0.37% | 0.74% | NA |
| Indica I | 595 | 85.00% | 13.80% | 0.50% | 0.67% | NA |
| Indica II | 465 | 83.20% | 11.80% | 3.23% | 1.72% | NA |
| Indica III | 913 | 68.70% | 27.60% | 3.07% | 0.66% | NA |
| Indica Intermediate | 786 | 71.10% | 26.80% | 1.53% | 0.51% | NA |
| Temperate Japonica | 767 | 2.60% | 97.30% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 3.70% | 95.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 54.40% | 42.20% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0629027213 | T -> C | LOC_Os06g48010.1 | 3_prime_UTR_variant ; 10.0bp to feature; MODIFIER | silent_mutation | Average:70.502; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0629027213 | T -> C | LOC_Os06g48000.1 | downstream_gene_variant ; 3721.0bp to feature; MODIFIER | silent_mutation | Average:70.502; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |
| vg0629027213 | T -> DEL | N | N | silent_mutation | Average:70.502; most accessible tissue: Zhenshan97 panicle, score: 82.888 | N | N | N | N |