| Variant ID: vg0823066655 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 23066655 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 107. )
CTGGTGTTCGCCATCAACGACGACGGCACGGGCGGCGTCTTCATCGACTCCGGCACGTCGCTCACCTGGCTCCAGCAGGACGCGTACGACGCCGTGCGCC[G/A]
CGAGCTGGTGTCCGTCCTCCGGCCGCTGCCGCCGACGAACGACACCGAGATCGGCCTGGAGACGTGCTTCCCGTGGCCGCCGCCGCCGAGCGTGGCCGTG
CACGGCCACGCTCGGCGGCGGCGGCCACGGGAAGCACGTCTCCAGGCCGATCTCGGTGTCGTTCGTCGGCGGCAGCGGCCGGAGGACGGACACCAGCTCG[C/T]
GGCGCACGGCGTCGTACGCGTCCTGCTGGAGCCAGGTGAGCGACGTGCCGGAGTCGATGAAGACGCCGCCCGTGCCGTCGTCGTTGATGGCGAACACCAG
| 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 | 53.30% | 46.40% | 0.11% | 0.25% | NA |
| All Indica | 2759 | 88.90% | 10.50% | 0.14% | 0.40% | NA |
| All Japonica | 1512 | 1.10% | 98.80% | 0.00% | 0.07% | NA |
| Aus | 269 | 1.90% | 98.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.30% | 0.17% | 0.67% | NA |
| Indica II | 465 | 91.40% | 7.30% | 0.22% | 1.08% | NA |
| Indica III | 913 | 88.90% | 11.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 80.00% | 19.60% | 0.13% | 0.25% | NA |
| Temperate Japonica | 767 | 1.60% | 98.30% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 0.60% | 99.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 44.40% | 54.40% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0823066655 | G -> A | LOC_Os08g36530.1 | missense_variant ; p.Arg341His; MODERATE | nonsynonymous_codon ; R341H | Average:68.765; most accessible tissue: Zhenshan97 flower, score: 81.46 | unknown | unknown | DELETERIOUS | 0.02 |
| vg0823066655 | G -> DEL | LOC_Os08g36530.1 | N | frameshift_variant | Average:68.765; most accessible tissue: Zhenshan97 flower, score: 81.46 | N | N | N | N |