| Variant ID: vg0823303282 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 23303282 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 241. )
GTCTGAAAAAGATGACCACATTTTTGATGTACACCAAGATGATAATTGTTCTGATACAGAACATGAAGTGCATGAAGGTAATGCTGATGAGGATCTAGAC[C/T]
ATTTGCAGGAAGATGGAGAAGTTACTATTATTGAAGCTAATTTAGAAGACCTTAACAACCAAGCTAACTTGACTGAAGACAGTAGGGATGATGCAGATGA
TCATCTGCATCATCCCTACTGTCTTCAGTCAAGTTAGCTTGGTTGTTAAGGTCTTCTAAATTAGCTTCAATAATAGTAACTTCTCCATCTTCCTGCAAAT[G/A]
GTCTAGATCCTCATCAGCATTACCTTCATGCACTTCATGTTCTGTATCAGAACAATTATCATCTTGGTGTACATCAAAAATGTGGTCATCTTTTTCAGAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.50% | 3.30% | 11.83% | 55.40% | NA |
| All Indica | 2759 | 1.40% | 0.10% | 11.16% | 87.35% | NA |
| All Japonica | 1512 | 85.80% | 10.00% | 3.04% | 1.19% | NA |
| Aus | 269 | 4.10% | 0.00% | 50.93% | 44.98% | NA |
| Indica I | 595 | 1.20% | 0.00% | 3.19% | 95.63% | NA |
| Indica II | 465 | 1.50% | 0.00% | 16.77% | 81.72% | NA |
| Indica III | 913 | 0.20% | 0.20% | 6.79% | 92.77% | NA |
| Indica Intermediate | 786 | 2.80% | 0.10% | 18.96% | 78.12% | NA |
| Temperate Japonica | 767 | 97.90% | 0.30% | 0.26% | 1.56% | NA |
| Tropical Japonica | 504 | 64.30% | 27.60% | 7.54% | 0.60% | NA |
| Japonica Intermediate | 241 | 92.10% | 4.10% | 2.49% | 1.24% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 55.21% | 30.21% | NA |
| Intermediate | 90 | 36.70% | 2.20% | 16.67% | 44.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0823303282 | C -> T | LOC_Os08g36880.1 | missense_variant ; p.His238Tyr; MODERATE | nonsynonymous_codon ; H238Y | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | TOLERATED | 0.06 |
| vg0823303282 | C -> DEL | LOC_Os08g36880.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |