| Variant ID: vg1012223963 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223963 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.71, T: 0.29, others allele: 0.00, population size: 38. )
CGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGGCGCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCG[T/C]
GAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAG
CTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTC[A/G]
CGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGCGCCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.90% | 15.80% | 2.35% | 50.97% | NA |
| All Indica | 2759 | 2.90% | 25.40% | 3.37% | 68.32% | NA |
| All Japonica | 1512 | 88.20% | 0.40% | 0.33% | 11.11% | NA |
| Aus | 269 | 0.70% | 8.90% | 2.97% | 87.36% | NA |
| Indica I | 595 | 4.00% | 6.60% | 2.69% | 86.72% | NA |
| Indica II | 465 | 3.40% | 28.00% | 7.10% | 61.51% | NA |
| Indica III | 913 | 1.60% | 32.40% | 1.64% | 64.29% | NA |
| Indica Intermediate | 786 | 3.10% | 30.20% | 3.69% | 63.10% | NA |
| Temperate Japonica | 767 | 95.40% | 0.30% | 0.26% | 4.04% | NA |
| Tropical Japonica | 504 | 81.50% | 0.20% | 0.20% | 18.06% | NA |
| Japonica Intermediate | 241 | 78.80% | 1.20% | 0.83% | 19.09% | NA |
| VI/Aromatic | 96 | 6.20% | 2.10% | 3.12% | 88.54% | NA |
| Intermediate | 90 | 43.30% | 14.40% | 2.22% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223963 | T -> C | LOC_Os10g23830.1 | synonymous_variant ; p.Arg19Arg; LOW | synonymous_codon | Average:12.598; most accessible tissue: Callus, score: 51.074 | N | N | N | N |
| vg1012223963 | T -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:12.598; most accessible tissue: Callus, score: 51.074 | N | N | N | N |