| Variant ID: vg0903406122 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3406122 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 241. )
GCGGTTGTACCTTCAAAAGCATCAACTGGCGCACCCAACGCCAAGGCTATACCTCGCATGATCTTTCTTGAAAGATCTACAAGTAAATTTTCATAACAAA[T/C]
GCTGTCACTCATAAGTAACAAATAATAAATGGATCAATAGCATACATGCACAAATAAAGATTTAAACTAAGTATAGAAGTTAACCTCTTAGAAGGCTGAT
ATCAGCCTTCTAAGAGGTTAACTTCTATACTTAGTTTAAATCTTTATTTGTGCATGTATGCTATTGATCCATTTATTATTTGTTACTTATGAGTGACAGC[A/G]
TTTGTTATGAAAATTTACTTGTAGATCTTTCAAGAAAGATCATGCGAGGTATAGCCTTGGCGTTGGGTGCGCCAGTTGATGCTTTTGAAGGTACAACCGC
| 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 | 63.90% | 36.10% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 0.90% | 98.90% | 0.13% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.90% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.50% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 7.30% | 92.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 47.80% | 50.00% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0903406122 | T -> C | LOC_Os09g07010.1 | upstream_gene_variant ; 3013.0bp to feature; MODIFIER | silent_mutation | Average:49.456; most accessible tissue: Zhenshan97 young leaf, score: 65.28 | N | N | N | N |
| vg0903406122 | T -> C | LOC_Os09g07030.1 | downstream_gene_variant ; 2758.0bp to feature; MODIFIER | silent_mutation | Average:49.456; most accessible tissue: Zhenshan97 young leaf, score: 65.28 | N | N | N | N |
| vg0903406122 | T -> C | LOC_Os09g07020.1 | intron_variant ; MODIFIER | silent_mutation | Average:49.456; most accessible tissue: Zhenshan97 young leaf, score: 65.28 | N | N | N | N |
| vg0903406122 | T -> C | LOC_Os09g07020.2 | intron_variant ; MODIFIER | silent_mutation | Average:49.456; most accessible tissue: Zhenshan97 young leaf, score: 65.28 | N | N | N | N |