| Variant ID: vg0611474546 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 11474546 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCGGGCAGTCTTCTTCCTCCTCTCTCCCTACTCCTCTCTGAGACGGTGGAAGAGAGGGTTGACAACGCTCCCTACGCCTCTCTCCTTCCCCTTTTCGGCA[T/C]
ATGGGTAGAAGAGGACGAAGCCATAGCCCTTAGATCTACCAGATTGCTTGTTGGAGATGACACAGCAGTCCTCGAGCTCACCGAAGAGGGAGAACGCAAA
TTTGCGTTCTCCCTCTTCGGTGAGCTCGAGGACTGCTGTGTCATCTCCAACAAGCAATCTGGTAGATCTAAGGGCTATGGCTTCGTCCTCTTCTACCCAT[A/G]
TGCCGAAAAGGGGAAGGAGAGAGGCGTAGGGAGCGTTGTCAACCCTCTCTTCCACCGTCTCAGAGAGGAGTAGGGAGAGAGGAGGAAGAAGACTGCCCGG
| 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 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.90% | 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 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0611474546 | T -> C | LOC_Os06g20010.1 | missense_variant ; p.Tyr66Cys; MODERATE | N | Average:73.162; most accessible tissue: Zhenshan97 young leaf, score: 88.878 | N | N | N | N |
| vg0611474546 | T -> C | LOC_Os06g20000.1 | upstream_gene_variant ; 4817.0bp to feature; MODIFIER | N | Average:73.162; most accessible tissue: Zhenshan97 young leaf, score: 88.878 | N | N | N | N |
| vg0611474546 | T -> C | LOC_Os06g20020.1 | upstream_gene_variant ; 1958.0bp to feature; MODIFIER | N | Average:73.162; most accessible tissue: Zhenshan97 young leaf, score: 88.878 | N | N | N | N |