| Variant ID: vg1200761918 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 761918 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TACAAGTTAATTAGAAAAACAACAAACTAAACTAACACTACTTAACGTATTTTCGCTATTATATCCGTTATTTTTGTTGCAAGTACAAGTTAAATTTAAA[C/T]
ATGTATATTTACGGACATGTATATTAATATTAATCTAGCTTATCATTTTGTTTTACTTTTTAATGGCTATTTAGGTGGGGGGCATGAAAGCAACAATGAG
CTCATTGTTGCTTTCATGCCCCCCACCTAAATAGCCATTAAAAAGTAAAACAAAATGATAAGCTAGATTAATATTAATATACATGTCCGTAAATATACAT[G/A]
TTTAAATTTAACTTGTACTTGCAACAAAAATAACGGATATAATAGCGAAAATACGTTAAGTAGTGTTAGTTTAGTTTGTTGTTTTTCTAATTAACTTGTA
| 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 | 99.60% | 0.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 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 | 97.80% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1200761918 | C -> T | LOC_Os12g02350.1 | upstream_gene_variant ; 1873.0bp to feature; MODIFIER | N | Average:29.281; most accessible tissue: Zhenshan97 flower, score: 73.946 | N | N | N | N |
| vg1200761918 | C -> T | LOC_Os12g02370.2 | downstream_gene_variant ; 4516.0bp to feature; MODIFIER | N | Average:29.281; most accessible tissue: Zhenshan97 flower, score: 73.946 | N | N | N | N |
| vg1200761918 | C -> T | LOC_Os12g02370.4 | downstream_gene_variant ; 4516.0bp to feature; MODIFIER | N | Average:29.281; most accessible tissue: Zhenshan97 flower, score: 73.946 | N | N | N | N |
| vg1200761918 | C -> T | LOC_Os12g02340.1 | intron_variant ; MODIFIER | N | Average:29.281; most accessible tissue: Zhenshan97 flower, score: 73.946 | N | N | N | N |
| vg1200761918 | C -> T | LOC_Os12g02340.2 | intron_variant ; MODIFIER | N | Average:29.281; most accessible tissue: Zhenshan97 flower, score: 73.946 | N | N | N | N |