| Variant ID: vg1115079183 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 15079183 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCCGTCGATGGAAGCCGAGCGCAGCGCTGCCGTTGACGGAAGCCGGGTGTATCGTCGGATGCCGAATATGCCGCGTCGCGCCGCTGCCGCCGCCGCCGCT[G/A]
GGCGTAGCACTGCCTCCACCGCCGGACGCCCTATGCCATCGCCACCACACTACCACGTAGGCCAGGGCACAAAGCTGCCATCCAATGGGTTGTGGAGGTA
TACCTCCACAACCCATTGGATGGCAGCTTTGTGCCCTGGCCTACGTGGTAGTGTGGTGGCGATGGCATAGGGCGTCCGGCGGTGGAGGCAGTGCTACGCC[C/T]
AGCGGCGGCGGCGGCAGCGGCGCGACGCGGCATATTCGGCATCCGACGATACACCCGGCTTCCGTCAACGGCAGCGCTGCGCTCGGCTTCCATCGACGGC
| 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 | 47.30% | 0.10% | 24.21% | 28.44% | NA |
| All Indica | 2759 | 38.00% | 0.10% | 32.33% | 29.54% | NA |
| All Japonica | 1512 | 63.60% | 0.00% | 5.95% | 30.42% | NA |
| Aus | 269 | 44.20% | 0.00% | 50.19% | 5.58% | NA |
| Indica I | 595 | 28.10% | 0.00% | 28.40% | 43.53% | NA |
| Indica II | 465 | 52.90% | 0.00% | 26.02% | 21.08% | NA |
| Indica III | 913 | 34.20% | 0.30% | 41.29% | 24.21% | NA |
| Indica Intermediate | 786 | 41.10% | 0.10% | 28.63% | 30.15% | NA |
| Temperate Japonica | 767 | 73.40% | 0.00% | 7.30% | 19.30% | NA |
| Tropical Japonica | 504 | 54.60% | 0.00% | 4.96% | 40.48% | NA |
| Japonica Intermediate | 241 | 51.50% | 0.00% | 3.73% | 44.81% | NA |
| VI/Aromatic | 96 | 59.40% | 0.00% | 8.33% | 32.29% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 21.11% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1115079183 | G -> A | LOC_Os11g26350.1 | missense_variant ; p.Gly12Arg; MODERATE | nonsynonymous_codon ; G12R | Average:19.034; most accessible tissue: Minghui63 panicle, score: 38.588 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1115079183 | G -> DEL | LOC_Os11g26350.1 | N | frameshift_variant | Average:19.034; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |