| Variant ID: vg0725680919 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 25680919 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAGAACAGAGTATTTCAAAGGTCCATTCGTTTCATTGACTCGTCCAAGTTCTGTAAAAAAAAAATATAAATAGTTCAAATGATCAATATTTCTAAGCAAA[A/G]
AAAAGATACATTTTTTCTAAAATAAAGCATTAATAAAGCTTTCTAAAATATTGAATTATTGGTGATGATAAATTTGTTTTCCATCAAGTGATTATCCAGA
TCTGGATAATCACTTGATGGAAAACAAATTTATCATCACCAATAATTCAATATTTTAGAAAGCTTTATTAATGCTTTATTTTAGAAAAAATGTATCTTTT[T/C]
TTTGCTTAGAAATATTGATCATTTGAACTATTTATATTTTTTTTTTACAGAACTTGGACGAGTCAATGAAACGAATGGACCTTTGAAATACTCTGTTCTG
| 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 | 68.00% | 0.20% | 5.97% | 25.84% | NA |
| All Indica | 2759 | 45.90% | 0.00% | 10.11% | 43.97% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 19.30% | 0.00% | 16.47% | 64.20% | NA |
| Indica II | 465 | 75.50% | 0.00% | 3.87% | 20.65% | NA |
| Indica III | 913 | 48.40% | 0.00% | 10.41% | 41.18% | NA |
| Indica Intermediate | 786 | 45.70% | 0.00% | 8.65% | 45.67% | 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 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 1.10% | 2.22% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0725680919 | A -> DEL | N | N | silent_mutation | Average:36.747; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |
| vg0725680919 | A -> G | LOC_Os07g42885.1 | upstream_gene_variant ; 4174.0bp to feature; MODIFIER | silent_mutation | Average:36.747; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |
| vg0725680919 | A -> G | LOC_Os07g42890.1 | downstream_gene_variant ; 1071.0bp to feature; MODIFIER | silent_mutation | Average:36.747; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |
| vg0725680919 | A -> G | LOC_Os07g42900.1 | downstream_gene_variant ; 2354.0bp to feature; MODIFIER | silent_mutation | Average:36.747; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |
| vg0725680919 | A -> G | LOC_Os07g42890.2 | downstream_gene_variant ; 1116.0bp to feature; MODIFIER | silent_mutation | Average:36.747; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |
| vg0725680919 | A -> G | LOC_Os07g42895.1 | intron_variant ; MODIFIER | silent_mutation | Average:36.747; most accessible tissue: Zhenshan97 flower, score: 60.838 | N | N | N | N |