| Variant ID: vg0233354640 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33354640 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCCGGGTCGATGTGGCACGGGTTCAGGAACCCGTGGTACATGTCGCGGCGCGGCTTGCGGCGCAGCGTGTCGGCGAGCGCGCCCAGGCGGTAGTACGTGT[C/T]
GTCGTCGATCTTGCCGGCGAAGTCGTAGCGCGGCTCGGCGCCGGCGGGGAACAGGCGCGGGAGGGCCGAGAAGTAGTCGTACGTCTTGCCGTCGTTCATG
CATGAACGACGGCAAGACGTACGACTACTTCTCGGCCCTCCCGCGCCTGTTCCCCGCCGGCGCCGAGCCGCGCTACGACTTCGCCGGCAAGATCGACGAC[G/A]
ACACGTACTACCGCCTGGGCGCGCTCGCCGACACGCTGCGCCGCAAGCCGCGCCGCGACATGTACCACGGGTTCCTGAACCCGTGCCACATCGACCCGGC
| 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 | 99.80% | 0.10% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.30% | 0.14% | 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 | 98.50% | 1.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 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 | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233354640 | C -> T | LOC_Os02g54450.1 | missense_variant ; p.Asp160Asn; MODERATE | N | Average:73.583; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | N | N | N | N |
| vg0233354640 | C -> T | LOC_Os02g54430.1 | upstream_gene_variant ; 3640.0bp to feature; MODIFIER | N | Average:73.583; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | N | N | N | N |
| vg0233354640 | C -> T | LOC_Os02g54440.1 | upstream_gene_variant ; 1199.0bp to feature; MODIFIER | N | Average:73.583; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | N | N | N | N |
| vg0233354640 | C -> T | LOC_Os02g54460.1 | upstream_gene_variant ; 1590.0bp to feature; MODIFIER | N | Average:73.583; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | N | N | N | N |
| vg0233354640 | C -> T | LOC_Os02g54470.1 | upstream_gene_variant ; 4704.0bp to feature; MODIFIER | N | Average:73.583; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | N | N | N | N |
| vg0233354640 | C -> T | LOC_Os02g54470.2 | upstream_gene_variant ; 4704.0bp to feature; MODIFIER | N | Average:73.583; most accessible tissue: Zhenshan97 young leaf, score: 84.624 | N | N | N | N |