| Variant ID: vg0233354792 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33354792 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CAGGCGCGGGAGGGCCGAGAAGTAGTCGTACGTCTTGCCGTCGTTCATGTTCTCGGTGCAGTTGAGCACGAGGATGTCGCCGTGGGTGATGATCTCCATC[G/A]
CCACCAGCACGGCGTCCTCCTCCTTGTCCAGGCTGCACATCACGAAGCGGACGTCGATGGCGGCGCGCCGCGGCGGCGGCTGGAGCGCGTACGCCATGCG
CGCATGGCGTACGCGCTCCAGCCGCCGCCGCGGCGCGCCGCCATCGACGTCCGCTTCGTGATGTGCAGCCTGGACAAGGAGGAGGACGCCGTGCTGGTGG[C/T]
GATGGAGATCATCACCCACGGCGACATCCTCGTGCTCAACTGCACCGAGAACATGAACGACGGCAAGACGTACGACTACTTCTCGGCCCTCCCGCGCCTG
| 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 | 99.50% | 0.40% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.70% | 0.25% | 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 | 96.60% | 2.40% | 1.08% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.40% | 0.25% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233354792 | G -> A | LOC_Os02g54450.1 | missense_variant ; p.Ala109Val; MODERATE | N | Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.448 | N | N | N | N |
| vg0233354792 | G -> A | LOC_Os02g54430.1 | upstream_gene_variant ; 3792.0bp to feature; MODIFIER | N | Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.448 | N | N | N | N |
| vg0233354792 | G -> A | LOC_Os02g54440.1 | upstream_gene_variant ; 1351.0bp to feature; MODIFIER | N | Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.448 | N | N | N | N |
| vg0233354792 | G -> A | LOC_Os02g54460.1 | upstream_gene_variant ; 1438.0bp to feature; MODIFIER | N | Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.448 | N | N | N | N |
| vg0233354792 | G -> A | LOC_Os02g54470.1 | upstream_gene_variant ; 4552.0bp to feature; MODIFIER | N | Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.448 | N | N | N | N |
| vg0233354792 | G -> A | LOC_Os02g54470.2 | upstream_gene_variant ; 4552.0bp to feature; MODIFIER | N | Average:71.374; most accessible tissue: Zhenshan97 root, score: 80.448 | N | N | N | N |