| Variant ID: vg0609243656 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9243656 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 61. )
ACACCGGCGCCCGATGTTGAGGCGGGCATCCGGCTCCCCATGCTGATCCTCCCGAGTCGACGGTGTAGACGAGGGAGTGGCAGCCGAATGACGTGCAGCC[G/A]
CCGCCGCTCGCCGCGCCCTCCGCCTTGATGACACGGAGCCGGTGGTAGCGGCGCCGGAGGTCTTGGTGGTGGTGGCGGACCGTCCACCAGCACCCAGGCG
CGCCTGGGTGCTGGTGGACGGTCCGCCACCACCACCAAGACCTCCGGCGCCGCTACCACCGGCTCCGTGTCATCAAGGCGGAGGGCGCGGCGAGCGGCGG[C/T]
GGCTGCACGTCATTCGGCTGCCACTCCCTCGTCTACACCGTCGACTCGGGAGGATCAGCATGGGGAGCCGGATGCCCGCCTCAACATCGGGCGCCGGTGT
| 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 | 3.90% | 0.10% | 7.19% | 88.79% | NA |
| All Indica | 2759 | 0.10% | 0.00% | 0.51% | 99.42% | NA |
| All Japonica | 1512 | 12.00% | 0.40% | 16.80% | 70.83% | NA |
| Aus | 269 | 0.00% | 0.00% | 24.16% | 75.84% | NA |
| Indica I | 595 | 0.20% | 0.00% | 0.34% | 99.50% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.22% | 99.78% | NA |
| Indica III | 913 | 0.00% | 0.00% | 0.44% | 99.56% | NA |
| Indica Intermediate | 786 | 0.10% | 0.00% | 0.89% | 98.98% | NA |
| Temperate Japonica | 767 | 21.80% | 0.80% | 27.77% | 49.67% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 1.39% | 97.62% | NA |
| Japonica Intermediate | 241 | 3.70% | 0.00% | 14.11% | 82.16% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 1.10% | 0.00% | 4.44% | 94.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609243656 | G -> A | LOC_Os06g16230.1 | missense_variant ; p.Ala152Val; MODERATE | nonsynonymous_codon ; A152V | Average:4.364; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.01 |
| vg0609243656 | G -> DEL | LOC_Os06g16230.1 | N | frameshift_variant | Average:4.364; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |