| Variant ID: vg1123253183 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23253183 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTGCTTCAGGTCGTCGTCGGAGAAGACCGGCCATTGCACCCTCTCGAACGCCAGGATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCT[G/C]
GCTTCTGCGGCTCGCCGGCGGCGGTGGCGGCCGCCGCCGCCGTCGTCTTCTTTGCCTCGTCGGCTGATGCCACCGCAGAGGCGTCCATGGATGATGGATC
GATCCATCATCCATGGACGCCTCTGCGGTGGCATCAGCCGACGAGGCAAAGAAGACGACGGCGGCGGCGGCCGCCACCGCCGCCGGCGAGCCGCAGAAGC[C/G]
AGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATCCTGGCGTTCGAGAGGGTGCAATGGCCGGTCTTCTCCGACGACGACCTGAAGCAC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.60% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1123253183 | G -> C | LOC_Os11g39060.1 | missense_variant ; p.Pro30Arg; MODERATE | N | Average:70.061; most accessible tissue: Minghui63 root, score: 82.818 | N | N | N | N |
| vg1123253183 | G -> C | LOC_Os11g39040.1 | upstream_gene_variant ; 4240.0bp to feature; MODIFIER | N | Average:70.061; most accessible tissue: Minghui63 root, score: 82.818 | N | N | N | N |
| vg1123253183 | G -> C | LOC_Os11g39050.1 | upstream_gene_variant ; 2668.0bp to feature; MODIFIER | N | Average:70.061; most accessible tissue: Minghui63 root, score: 82.818 | N | N | N | N |
| vg1123253183 | G -> C | LOC_Os11g39070.1 | downstream_gene_variant ; 2603.0bp to feature; MODIFIER | N | Average:70.061; most accessible tissue: Minghui63 root, score: 82.818 | N | N | N | N |