| Variant ID: vg0221477243 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21477243 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGTTGGATGCGCGGGCTGATCTGGTGGCCGCCCCCCGCTCAGCGGATCATCGCGCACGACCTGCAAACCATTTTCGATTAATTCCTCGCGTGCACACCAA[C/A]
AGATTAAATCCCTGAAGAATCAATTCACGAAACGGATCAATCTCTTTCCGAGGAACAGAAAATTAACTGAAAAGAAATTAAAATCAACGCACAATTTCCA
TGGAAATTGTGCGTTGATTTTAATTTCTTTTCAGTTAATTTTCTGTTCCTCGGAAAGAGATTGATCCGTTTCGTGAATTGATTCTTCAGGGATTTAATCT[G/T]
TTGGTGTGCACGCGAGGAATTAATCGAAAATGGTTTGCAGGTCGTGCGCGATGATCCGCTGAGCGGGGGGCGGCCACCAGATCAGCCCGCGCATCCAACT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.10% | 0.80% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 98.50% | 1.30% | 0.22% | 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 | 99.50% | 0.00% | 0.50% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.80% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221477243 | C -> A | LOC_Os02g35760.1 | 5_prime_UTR_variant ; 130.0bp to feature; MODIFIER | silent_mutation | Average:69.191; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 | N | N | N | N |
| vg0221477243 | C -> A | LOC_Os02g35750.1 | downstream_gene_variant ; 3421.0bp to feature; MODIFIER | silent_mutation | Average:69.191; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 | N | N | N | N |
| vg0221477243 | C -> A | LOC_Os02g35750.2 | downstream_gene_variant ; 1775.0bp to feature; MODIFIER | silent_mutation | Average:69.191; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 | N | N | N | N |
| vg0221477243 | C -> A | LOC_Os02g35750.3 | downstream_gene_variant ; 1610.0bp to feature; MODIFIER | silent_mutation | Average:69.191; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 | N | N | N | N |
| vg0221477243 | C -> A | LOC_Os02g35760.2 | intron_variant ; MODIFIER | silent_mutation | Average:69.191; most accessible tissue: Zhenshan97 flag leaf, score: 78.259 | N | N | N | N |