| Variant ID: vg1012224034 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224034 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.03, others allele: 0.00, population size: 59. )
AGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCG[A/G]
GAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATG
CATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTC[T/C]
CGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCT
| 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 | 31.30% | 17.70% | 1.04% | 49.98% | NA |
| All Indica | 2759 | 2.70% | 28.50% | 1.59% | 67.27% | NA |
| All Japonica | 1512 | 89.30% | 0.40% | 0.00% | 10.32% | NA |
| Aus | 269 | 4.10% | 9.30% | 1.12% | 85.50% | NA |
| Indica I | 595 | 3.70% | 7.10% | 3.03% | 86.22% | NA |
| Indica II | 465 | 3.20% | 35.90% | 1.51% | 59.35% | NA |
| Indica III | 913 | 1.50% | 33.50% | 0.77% | 64.18% | NA |
| Indica Intermediate | 786 | 2.90% | 34.40% | 1.53% | 61.20% | NA |
| Temperate Japonica | 767 | 97.00% | 0.30% | 0.00% | 2.74% | NA |
| Tropical Japonica | 504 | 81.50% | 0.40% | 0.00% | 18.06% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.80% | 0.00% | 18.26% | NA |
| VI/Aromatic | 96 | 6.20% | 3.10% | 1.04% | 89.58% | NA |
| Intermediate | 90 | 43.30% | 17.80% | 1.11% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224034 | A -> G | LOC_Os10g23830.1 | missense_variant ; p.Glu43Gly; MODERATE | nonsynonymous_codon ; E43G | Average:13.887; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 0.26 |
| vg1012224034 | A -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:13.887; most accessible tissue: Callus, score: 51.074 | N | N | N | N |