| Variant ID: vg0221167589 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21167589 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGTATGTATATCCATTCTAGTTGTATTCAAAAGTCAAAACTCAAGTTAACACATTAGTTTAAAGCACTCACAATGAAGTTAGCTTGCAACATATGGTTGA[A/G]
GAGATAATATCCGCCAAAAAAAGGTTCATTGCATCATACACCTTGACGTAGGGAGATTAGTCTGTTCCTTTGTATAATAATTCATCTTTCGCTTTGGAGG
CCTCCAAAGCGAAAGATGAATTATTATACAAAGGAACAGACTAATCTCCCTACGTCAAGGTGTATGATGCAATGAACCTTTTTTTGGCGGATATTATCTC[T/C]
TCAACCATATGTTGCAAGCTAACTTCATTGTGAGTGCTTTAAACTAATGTGTTAACTTGAGTTTTGACTTTTGAATACAACTAGAATGGATATACATACC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 94.60% | 5.40% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 82.30% | 17.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221167589 | A -> G | LOC_Os02g35200.1 | downstream_gene_variant ; 1903.0bp to feature; MODIFIER | silent_mutation | Average:52.637; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0221167589 | A -> G | LOC_Os02g35220.1 | downstream_gene_variant ; 2940.0bp to feature; MODIFIER | silent_mutation | Average:52.637; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |
| vg0221167589 | A -> G | LOC_Os02g35210.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.637; most accessible tissue: Minghui63 flag leaf, score: 67.099 | N | N | N | N |