| Variant ID: vg1012223933 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223933 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGGAGCAGCCGCCGCCGACGAGGTTGTCCACGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGGCGCGGATGCGGACACGGTCGGG[G/A]
AGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCG
CGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCT[C/T]
CCCGACCGTGTCCGCATCCGCGCCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCGTGGACAACCTCGTCGGCGGCGGCTGCTCCC
| 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 | 49.60% | 0.00% | 1.02% | 49.34% | NA |
| All Indica | 2759 | 32.80% | 0.00% | 1.30% | 65.82% | NA |
| All Japonica | 1512 | 88.80% | 0.00% | 0.07% | 11.11% | NA |
| Aus | 269 | 11.90% | 0.00% | 2.60% | 85.50% | NA |
| Indica I | 595 | 14.30% | 0.00% | 0.84% | 84.87% | NA |
| Indica II | 465 | 40.60% | 0.00% | 2.37% | 56.99% | NA |
| Indica III | 913 | 36.00% | 0.10% | 1.53% | 62.32% | NA |
| Indica Intermediate | 786 | 38.50% | 0.00% | 0.76% | 60.69% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 81.70% | 0.00% | 0.20% | 18.06% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 0.00% | 18.67% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 2.22% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223933 | G -> A | LOC_Os10g23830.1 | synonymous_variant ; p.Gly9Gly; LOW | synonymous_codon | Average:11.099; most accessible tissue: Callus, score: 51.074 | N | N | N | N |
| vg1012223933 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:11.099; most accessible tissue: Callus, score: 51.074 | N | N | N | N |