| Variant ID: vg1124756852 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24756852 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCAAGGTCGGCGGCGAGACGTTCCCGGCGCACCGGTGCGTCCTCGCGGCGCGGTCGCCGGTGTTCAGGGCGGAGCTCCTCGGCCCCATGAGGGAGCACGC[C/T]
GCGACGACCATCCGCGTCGACGACATGGACGCCTCCGTGTTCGCCGCTCTGCTGCGCTTCGTCTACACCGACGAGCTGCCGGAGCTGGACGGCGGCAGCG
CGCTGCCGCCGTCCAGCTCCGGCAGCTCGTCGGTGTAGACGAAGCGCAGCAGAGCGGCGAACACGGAGGCGTCCATGTCGTCGACGCGGATGGTCGTCGC[G/A]
GCGTGCTCCCTCATGGGGCCGAGGAGCTCCGCCCTGAACACCGGCGACCGCGCCGCGAGGACGCACCGGTGCGCCGGGAACGTCTCGCCGCCGACCTTGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 91.80% | 8.20% | 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 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.00% | 12.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1124756852 | C -> T | LOC_Os11g41300.1 | synonymous_variant ; p.Ala229Ala; LOW | synonymous_codon | Average:75.891; most accessible tissue: Minghui63 flag leaf, score: 85.836 | N | N | N | N |