| Variant ID: vg1012223906 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223906 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GAATCACACCAAAAAAAAAAAATATCAGGGAGCAGCCGCCGCCGACGAGGTTGTCCACGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACC[A/G]
ATGGCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGG
CCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGCCAT[T/C]
GGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCGTGGACAACCTCGTCGGCGGCGGCTGCTCCCTGATATTTTTTTTTTTTGGTGTGATTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.80% | 0.10% | 0.74% | 49.28% | NA |
| All Indica | 2759 | 33.50% | 0.10% | 0.72% | 65.71% | NA |
| All Japonica | 1512 | 88.60% | 0.10% | 0.13% | 11.18% | NA |
| Aus | 269 | 10.00% | 0.70% | 4.09% | 85.13% | NA |
| Indica I | 595 | 14.60% | 0.20% | 0.67% | 84.54% | NA |
| Indica II | 465 | 42.20% | 0.00% | 0.86% | 56.99% | NA |
| Indica III | 913 | 37.00% | 0.20% | 0.44% | 62.32% | NA |
| Indica Intermediate | 786 | 38.40% | 0.00% | 1.02% | 60.56% | NA |
| Temperate Japonica | 767 | 95.70% | 0.00% | 0.00% | 4.30% | NA |
| Tropical Japonica | 504 | 82.10% | 0.00% | 0.00% | 17.86% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.40% | 0.83% | 19.09% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 62.20% | 1.10% | 0.00% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223906 | A -> G | LOC_Os10g23830.1 | upstream_gene_variant ; 1.0bp to feature; MODIFIER | silent_mutation | Average:8.866; most accessible tissue: Callus, score: 26.513 | N | N | N | N |
| vg1012223906 | A -> G | LOC_Os10g23840.1 | upstream_gene_variant ; 1063.0bp to feature; MODIFIER | silent_mutation | Average:8.866; most accessible tissue: Callus, score: 26.513 | N | N | N | N |
| vg1012223906 | A -> G | LOC_Os10g23820-LOC_Os10g23830 | intergenic_region ; MODIFIER | silent_mutation | Average:8.866; most accessible tissue: Callus, score: 26.513 | N | N | N | N |
| vg1012223906 | A -> DEL | N | N | silent_mutation | Average:8.866; most accessible tissue: Callus, score: 26.513 | N | N | N | N |