| Variant ID: vg1123253110 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23253110 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CGGCGAGGTCGTCGTCCAAAGCCTTGTGCAGGGCGGCCATCTTGTCGATCTCCCGGCGCTGCTCCGGCGAGAGGTGCTTCAGGTCGTCGTCGGAGAAGAC[C/A]
GGCCATTGCACCCTCTCGAACGCCAGGATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGG
CCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATCCTGGCGTTCGAGAGGGTGCAATGGCC[G/T]
GTCTTCTCCGACGACGACCTGAAGCACCTCTCGCCGGAGCAGCGCCGGGAGATCGACAAGATGGCCGCCCTGCACAAGGCTTTGGACGACGACCTCGCCG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 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 | 100.00% | 0.00% | 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 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1123253110 | C -> A | LOC_Os11g39060.1 | synonymous_variant ; p.Pro54Pro; LOW | N | Average:69.051; most accessible tissue: Minghui63 root, score: 83.538 | N | N | N | N |
| vg1123253110 | C -> A | LOC_Os11g39040.1 | upstream_gene_variant ; 4167.0bp to feature; MODIFIER | N | Average:69.051; most accessible tissue: Minghui63 root, score: 83.538 | N | N | N | N |
| vg1123253110 | C -> A | LOC_Os11g39050.1 | upstream_gene_variant ; 2595.0bp to feature; MODIFIER | N | Average:69.051; most accessible tissue: Minghui63 root, score: 83.538 | N | N | N | N |
| vg1123253110 | C -> A | LOC_Os11g39070.1 | downstream_gene_variant ; 2676.0bp to feature; MODIFIER | N | Average:69.051; most accessible tissue: Minghui63 root, score: 83.538 | N | N | N | N |