| Variant ID: vg1100141411 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 141411 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGGTGCAAGACTTCCGTCGCGTCTGGGAACATCGCTTTAACAGCTAAGGGCATCCACAATGCTATTATTTGGTAATAAGTAATGCTACTACTTAACTGCA[G/A]
CAACTGTATGTCCCATGCGTTATACGGAGGGACCTATCCCAAGATATGCTCGCCCCGACGATGCCTTGCAGATCCTCTCTCTCCAAGTGATAGAAGCAAA
TTTGCTTCTATCACTTGGAGAGAGAGGATCTGCAAGGCATCGTCGGGGCGAGCATATCTTGGGATAGGTCCCTCCGTATAACGCATGGGACATACAGTTG[C/T]
TGCAGTTAAGTAGTAGCATTACTTATTACCAAATAATAGCATTGTGGATGCCCTTAGCTGTTAAAGCGATGTTCCCAGACGCGACGGAAGTCTTGCACCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.10% | 0.10% | 0.28% | 1.52% | NA |
| All Indica | 2759 | 99.30% | 0.00% | 0.25% | 0.43% | NA |
| All Japonica | 1512 | 95.50% | 0.30% | 0.40% | 3.84% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.00% | 0.17% | NA |
| Indica II | 465 | 98.70% | 0.00% | 0.65% | 0.65% | NA |
| Indica III | 913 | 99.80% | 0.00% | 0.11% | 0.11% | NA |
| Indica Intermediate | 786 | 98.70% | 0.00% | 0.38% | 0.89% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 87.50% | 0.00% | 0.99% | 11.51% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.70% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 2.20% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1100141411 | G -> A | LOC_Os11g01250.1 | upstream_gene_variant ; 1093.0bp to feature; MODIFIER | silent_mutation | Average:68.961; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg1100141411 | G -> A | LOC_Os11g01240.1 | downstream_gene_variant ; 2452.0bp to feature; MODIFIER | silent_mutation | Average:68.961; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg1100141411 | G -> A | LOC_Os11g01270.1 | downstream_gene_variant ; 2754.0bp to feature; MODIFIER | silent_mutation | Average:68.961; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg1100141411 | G -> A | LOC_Os11g01260.1 | intron_variant ; MODIFIER | silent_mutation | Average:68.961; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |
| vg1100141411 | G -> DEL | N | N | silent_mutation | Average:68.961; most accessible tissue: Zhenshan97 flower, score: 87.172 | N | N | N | N |