| Variant ID: vg0424682148 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 24682148 |
| 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: 291. )
CCAACTGATCGTAATCCTCGTCAGTCTTGTCCTCAACTCCGACGATTTTTCTTTTGCCTGGGAGAACCACTTGACGCTTAGGCTCATCAGGCCCTCTGCC[C/T]
TTCTTTCCTTTGCTAGACATGTCCTTCACGAAAAAGACTTGCGTTACATCATTGGCAAGGACAAAAGGTTCGTCCGAGTATCCAACCTTGTTAAGGTCAA
TTGACCTTAACAAGGTTGGATACTCGGACGAACCTTTTGTCCTTGCCAATGATGTAACGCAAGTCTTTTTCGTGAAGGACATGTCTAGCAAAGGAAAGAA[G/A]
GGCAGAGGGCCTGATGAGCCTAAGCGTCAAGTGGTTCTCCCAGGCAAAAGAAAAATCGTCGGAGTTGAGGACAAGACTGACGAGGATTACGATCAGTTGG
| 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 | 71.80% | 0.00% | 19.30% | 8.89% | NA |
| All Indica | 2759 | 52.30% | 0.10% | 32.55% | 15.11% | NA |
| All Japonica | 1512 | 99.70% | 0.00% | 0.20% | 0.07% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 34.50% | 0.00% | 54.45% | 11.09% | NA |
| Indica II | 465 | 33.50% | 0.00% | 38.71% | 27.74% | NA |
| Indica III | 913 | 75.90% | 0.20% | 13.25% | 10.62% | NA |
| Indica Intermediate | 786 | 49.40% | 0.00% | 34.73% | 15.90% | NA |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 0.00% | 12.22% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0424682148 | C -> DEL | LOC_Os04g41599.1 | N | frameshift_variant | Average:4.359; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0424682148 | C -> T | LOC_Os04g41599.1 | synonymous_variant ; p.Lys905Lys; LOW | synonymous_codon | Average:4.359; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |