| Variant ID: vg0801635240 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1635240 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACCGGATCGTGCTCGCCATGCGCTCGCCGGTGTTCATGGCATCGCTGTACGGGTCGATGAGGGAGCACCGCGCGCCGCGGATCGCCGTCGACGACATGGA[G/A]
CCGGAGGTGTTCGACGCGCTCCTCCGCTTCGTCTACAGCGACACGCTGGCGCTCCCCGGCGACCTCGGGGAAGGCGAGTACAAGGAGATGGTGCGGCAGC
GCTGCCGCACCATCTCCTTGTACTCGCCTTCCCCGAGGTCGCCGGGGAGCGCCAGCGTGTCGCTGTAGACGAAGCGGAGGAGCGCGTCGAACACCTCCGG[C/T]
TCCATGTCGTCGACGGCGATCCGCGGCGCGCGGTGCTCCCTCATCGACCCGTACAGCGATGCCATGAACACCGGCGAGCGCATGGCGAGCACGATCCGGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.20% | 0.10% | 0.72% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 0.10% | 1.20% | 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 | 97.60% | 0.00% | 2.35% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.00% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 0.40% | 1.40% | 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 | 96.70% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0801635240 | G -> A | LOC_Os08g03490.1 | synonymous_variant ; p.Glu246Glu; LOW | N | Average:76.438; most accessible tissue: Zhenshan97 root, score: 83.59 | N | N | N | N |
| vg0801635240 | G -> A | LOC_Os08g03500.1 | upstream_gene_variant ; 3940.0bp to feature; MODIFIER | N | Average:76.438; most accessible tissue: Zhenshan97 root, score: 83.59 | N | N | N | N |
| vg0801635240 | G -> A | LOC_Os08g03470.1 | downstream_gene_variant ; 4067.0bp to feature; MODIFIER | N | Average:76.438; most accessible tissue: Zhenshan97 root, score: 83.59 | N | N | N | N |
| vg0801635240 | G -> A | LOC_Os08g03480.1 | downstream_gene_variant ; 2100.0bp to feature; MODIFIER | N | Average:76.438; most accessible tissue: Zhenshan97 root, score: 83.59 | N | N | N | N |