Search for Variation information by Variation ID:
Detailed information for vg0435227422:
| Variant ID: vg0435227422 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 35227422 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCAGCTTCGGCCGCCCTCGGGTCCGCCGCTCGGTCAGGGCGGCGGGACAGGAGGAGGAAGAAGAGGTCGGCCCATTCCGACGACGAGGGTCATGTCCTC[G/A]
CCTTCGAAGGCGTTTCGCTGGCCACCCGAAAGGGGAGGCCTGCGAGCGACCAAAAGAAGGAAGCCGACGCTCCCTGACCTCGGCTACTTGGAAGAACGAA
Reverse complement sequence
TTCGTTCTTCCAAGTAGCCGAGGTCAGGGAGCGTCGGCTTCCTTCTTTTGGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCAGCGAAACGCCTTCGAAGG[C/T]
GAGGACATGACCCTCGTCGTCGGAATGGGCCGACCTCTTCTTCCTCCTCCTGTCCCGCCGCCCTGACCGAGCGGCGGACCCGAGGGCGGCCGAAGCTGCC
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 | 46.00% | 0.10% | 1.78% | 52.09% | NA |
| All Indica | 2759 | 10.40% | 0.20% | 2.32% | 87.02% | NA |
| All Japonica | 1512 | 97.90% | 0.00% | 1.19% | 0.86% | NA |
| Aus | 269 | 91.10% | 0.00% | 0.00% | 8.92% | NA |
| Indica I | 595 | 7.10% | 0.00% | 1.85% | 91.09% | NA |
| Indica II | 465 | 5.80% | 0.00% | 1.94% | 92.26% | NA |
| Indica III | 913 | 8.90% | 0.20% | 2.85% | 88.06% | NA |
| Indica Intermediate | 786 | 17.60% | 0.50% | 2.29% | 79.64% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 96.20% | 0.00% | 1.79% | 1.98% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 3.73% | 0.83% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 81.10% | 1.10% | 1.11% | 16.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0435227422 | G -> DEL | LOC_Os04g59220.1 | N | frameshift_variant | Average:6.408; most accessible tissue: Callus, score: 14.467 | N | N | N | N |
| vg0435227422 | G -> A | LOC_Os04g59220.1 | missense_variant ; p.Ala441Thr; MODERATE | nonsynonymous_codon ; A441T | Average:6.408; most accessible tissue: Callus, score: 14.467 | possibly damaging  |
1.571 |
DELETERIOUS | 0.01 |