| Variant ID: vg0234178688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34178688 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 309. )
ACGTTAGGTGATTTCGACCCTAACTACGTGTCGAGGTCATTCCCAACTGGTGAGTATGATGCCACCGGATCGGCTCCAACACCACCAGTTATGGAGCCAC[C/T]
GGCGGGTTCAGAAGCATCCGGCACTATGAGTGGGAGTGCATCGACGAACACCGGCTCAAAGAGATCAAGAACTTCCGGTGTTTGGCAACATTTCGATGAG
CTCATCGAAATGTTGCCAAACACCGGAAGTTCTTGATCTCTTTGAGCCGGTGTTCGTCGATGCACTCCCACTCATAGTGCCGGATGCTTCTGAACCCGCC[G/A]
GTGGCTCCATAACTGGTGGTGTTGGAGCCGATCCGGTGGCATCATACTCACCAGTTGGGAATGACCTCGACACGTAGTTAGGGTCGAAATCACCTAACGT
| 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 | 33.40% | 0.20% | 18.41% | 47.95% | NA |
| All Indica | 2759 | 3.10% | 0.40% | 25.48% | 71.08% | NA |
| All Japonica | 1512 | 93.70% | 0.00% | 3.24% | 3.11% | NA |
| Aus | 269 | 6.30% | 0.00% | 29.37% | 64.31% | NA |
| Indica I | 595 | 2.00% | 0.00% | 15.80% | 82.18% | NA |
| Indica II | 465 | 3.00% | 0.60% | 12.69% | 83.66% | NA |
| Indica III | 913 | 4.30% | 0.40% | 38.99% | 56.30% | NA |
| Indica Intermediate | 786 | 2.50% | 0.40% | 24.68% | 72.39% | NA |
| Temperate Japonica | 767 | 96.00% | 0.00% | 0.13% | 3.91% | NA |
| Tropical Japonica | 504 | 89.90% | 0.00% | 9.33% | 0.79% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 0.41% | 5.39% | NA |
| VI/Aromatic | 96 | 20.80% | 1.00% | 25.00% | 53.12% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 16.67% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234178688 | C -> T | LOC_Os02g55830.1 | missense_variant ; p.Pro43Leu; MODERATE | nonsynonymous_codon ; P43L | Average:5.041; most accessible tissue: Minghui63 panicle, score: 16.27 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0234178688 | C -> DEL | LOC_Os02g55830.1 | N | frameshift_variant | Average:5.041; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |