| Variant ID: vg1007671788 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 7671788 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 386. )
GATCGTCCAATTTAACATACTTACTTATCCTCGCTGAATAGCCCGATGGAACTTTAATATCCTTCAAGCATGATAACATTGCGATCTTCTCATCCTTCGA[C/A]
AGTGTGTGGCAGGCTGGAGGGACGTACACTTTACTTGTCTCTGCATCTCGTATGGGCTGGAGTTCGCTGCGAATATTCATGTCCTGTAGATCAAGGCGCG
CGCGCCTTGATCTACAGGACATGAATATTCGCAGCGAACTCCAGCCCATACGAGATGCAGAGACAAGTAAAGTGTACGTCCCTCCAGCCTGCCACACACT[G/T]
TCGAAGGATGAGAAGATCGCAATGTTATCATGCTTGAAGGATATTAAAGTTCCATCGGGCTATTCAGCGAGGATAAGTAAGTATGTTAAATTGGACGATC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.40% | 0.10% | 7.62% | 78.82% | NA |
| All Indica | 2759 | 1.30% | 0.20% | 3.77% | 94.74% | NA |
| All Japonica | 1512 | 38.60% | 0.00% | 1.39% | 59.99% | NA |
| Aus | 269 | 0.40% | 0.00% | 73.61% | 26.02% | NA |
| Indica I | 595 | 0.70% | 0.20% | 0.50% | 98.66% | NA |
| Indica II | 465 | 0.90% | 0.00% | 1.51% | 97.63% | NA |
| Indica III | 913 | 1.50% | 0.50% | 5.04% | 92.88% | NA |
| Indica Intermediate | 786 | 1.70% | 0.00% | 6.11% | 92.24% | NA |
| Temperate Japonica | 767 | 53.50% | 0.00% | 1.04% | 45.50% | NA |
| Tropical Japonica | 504 | 8.50% | 0.00% | 1.79% | 89.68% | NA |
| Japonica Intermediate | 241 | 54.40% | 0.00% | 1.66% | 43.98% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 28.12% | 71.88% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 11.11% | 72.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1007671788 | C -> A | LOC_Os10g14130.1 | synonymous_variant ; p.Leu151Leu; LOW | synonymous_codon | Average:6.753; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg1007671788 | C -> DEL | LOC_Os10g14130.1 | N | frameshift_variant | Average:6.753; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |