Search for Variation information by Variation ID:
Detailed information for vg0512045288:
| Variant ID: vg0512045288 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045288 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGGAATTGTTGCGCTTGGATTCCTCTTCTTCATCACTACTTATGATGATGACCGGAGGATCCGCTTGAGCTGGGGCAACTTCTTTCTCCACCACACGAA[C/A]
CTTTGGCGCCAGTTGATAGCGAGGGACAAATAGAGCTCTCTTCCTTGCGGTAAGACGAATCCTGGCCTTCTGCGGCGGTGCTTCTCCCTTCAATGCGGCT
Reverse complement sequence
AGCCGCATTGAAGGGAGAAGCACCGCCGCAGAAGGCCAGGATTCGTCTTACCGCAAGGAAGAGAGCTCTATTTGTCCCTCGCTATCAACTGGCGCCAAAG[G/T]
TTCGTGTGGTGGAGAAAGAAGTTGCCCCAGCTCAAGCGGATCCTCCGGTCATCATCATAAGTAGTGATGAAGAAGAGGAATCCAAGCGCAACAATTCCAA
Allele Frequencies:
| 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 | 84.70% | 0.10% | 4.17% | 11.05% | NA |
| All Indica | 2759 | 86.20% | 0.20% | 6.27% | 7.32% | NA |
| All Japonica | 1512 | 91.90% | 0.00% | 0.13% | 7.94% | NA |
| Aus | 269 | 23.00% | 0.00% | 5.58% | 71.38% | NA |
| Indica I | 595 | 92.10% | 0.00% | 3.19% | 4.71% | NA |
| Indica II | 465 | 97.60% | 0.00% | 1.08% | 1.29% | NA |
| Indica III | 913 | 76.20% | 0.50% | 12.92% | 10.30% | NA |
| Indica Intermediate | 786 | 86.50% | 0.10% | 3.94% | 9.41% | NA |
| Temperate Japonica | 767 | 85.40% | 0.00% | 0.26% | 14.34% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 87.80% | 0.00% | 4.44% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045288 | C -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:22.474; most accessible tissue: Minghui63 young leaf, score: 32.638 | N | N | N | N |
| vg0512045288 | C -> A | LOC_Os05g20520.1 | missense_variant ; p.Val232Phe; MODERATE | nonsynonymous_codon ; V232F | Average:22.474; most accessible tissue: Minghui63 young leaf, score: 32.638 | probably damaging  |
2.059 |
DELETERIOUS | 0.04 |