| Variant ID: vg1001932853 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1932853 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTTGTTGTAGATCCATTCTTGTCATGAAATAAAGCTGTAGCAGAAGATACATACTTAGTATAAGGTGATATTCGTGATTCCCACGTTGCTATTTCAAAAT[C/G]
ACCACCTGAAATTGCCACCGATCTAGCTATTACCTCTTTGAACGATATACTTGGTTTCTTATAGTTTGGAATATCATCCCTTTCTACTCGAGGTGGCTTT
AAAGCCACCTCGAGTAGAAAGGGATGATATTCCAAACTATAAGAAACCAAGTATATCGTTCAAAGAGGTAATAGCTAGATCGGTGGCAATTTCAGGTGGT[G/C]
ATTTTGAAATAGCAACGTGGGAATCACGAATATCACCTTATACTAAGTATGTATCTTCTGCTACAGCTTTATTTCATGACAAGAATGGATCTACAACAAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.90% | 0.10% | 0.80% | 14.18% | NA |
| All Indica | 2759 | 78.30% | 0.00% | 1.05% | 20.70% | NA |
| All Japonica | 1512 | 99.00% | 0.40% | 0.13% | 0.46% | NA |
| Aus | 269 | 66.90% | 0.00% | 2.60% | 30.48% | NA |
| Indica I | 595 | 61.30% | 0.00% | 2.02% | 36.64% | NA |
| Indica II | 465 | 85.60% | 0.00% | 0.22% | 14.19% | NA |
| Indica III | 913 | 80.90% | 0.00% | 0.88% | 18.18% | NA |
| Indica Intermediate | 786 | 83.60% | 0.00% | 1.02% | 15.39% | NA |
| Temperate Japonica | 767 | 98.40% | 0.70% | 0.26% | 0.65% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001932853 | C -> G | LOC_Os10g04140.1 | upstream_gene_variant ; 4919.0bp to feature; MODIFIER | silent_mutation | Average:32.203; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg1001932853 | C -> G | LOC_Os10g04150.1 | upstream_gene_variant ; 1914.0bp to feature; MODIFIER | silent_mutation | Average:32.203; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg1001932853 | C -> G | LOC_Os10g04160.1 | intron_variant ; MODIFIER | silent_mutation | Average:32.203; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |
| vg1001932853 | C -> DEL | N | N | silent_mutation | Average:32.203; most accessible tissue: Zhenshan97 young leaf, score: 63.653 | N | N | N | N |