Search for Variation information by Variation ID:
Detailed information for vg0512045386:
| Variant ID: vg0512045386 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045386 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AACCTTTGGCGCCAGTTGATAGCGAGGGACAAATAGAGCTCTCTTCCTTGCGGTAAGACGAATCCTGGCCTTCTGCGGCGGTGCTTCTCCCTTCAATGCG[G/A]
CTAATTCCTTCTCCAAACGATCCACCTTGTCTTCTAGCTTGCAAATCTTACCACGATTCCGGTCTTCACGATCTTGAGCGGCTAACACAGTCTCCGCACG
Reverse complement sequence
CGTGCGGAGACTGTGTTAGCCGCTCAAGATCGTGAAGACCGGAATCGTGGTAAGATTTGCAAGCTAGAAGACAAGGTGGATCGTTTGGAGAAGGAATTAG[C/T]
CGCATTGAAGGGAGAAGCACCGCCGCAGAAGGCCAGGATTCGTCTTACCGCAAGGAAGAGAGCTCTATTTGTCCCTCGCTATCAACTGGCGCCAAAGGTT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.20% | 1.50% | 6.35% | 9.99% | NA |
| All Indica | 2759 | 86.10% | 2.40% | 8.74% | 2.83% | NA |
| All Japonica | 1512 | 84.90% | 0.10% | 3.17% | 11.90% | NA |
| Aus | 269 | 21.60% | 0.70% | 0.74% | 76.95% | NA |
| Indica I | 595 | 91.90% | 0.30% | 7.73% | 0.00% | NA |
| Indica II | 465 | 97.60% | 0.00% | 0.86% | 1.51% | NA |
| Indica III | 913 | 76.30% | 5.80% | 13.36% | 4.49% | NA |
| Indica Intermediate | 786 | 86.10% | 1.30% | 8.78% | 3.82% | NA |
| Temperate Japonica | 767 | 72.50% | 0.00% | 5.61% | 21.90% | NA |
| Tropical Japonica | 504 | 99.20% | 0.20% | 0.20% | 0.40% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.00% | 1.66% | 4.15% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 84.40% | 2.20% | 6.67% | 6.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045386 | G -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:16.235; most accessible tissue: Zhenshan97 flower, score: 24.143 | N | N | N | N |
| vg0512045386 | G -> A | LOC_Os05g20520.1 | missense_variant ; p.Ala199Val; MODERATE | nonsynonymous_codon ; A199V | Average:16.235; most accessible tissue: Zhenshan97 flower, score: 24.143 | benign  |
1.372 |
DELETERIOUS | 0.01 |