Search for Variation information by Variation ID:
Detailed information for vg0414145792:
| Variant ID: vg0414145792 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14145792 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 245. )
Flanking Sequence (100 bp) in Reference Genome:
TACGGACCCTCCCACATTGGTGAGAGCTTGCTCAATCCAGCACGCGTTTGAACGCGGCGTAAGACGAGGTCGTCGACGCAGAGTGATCGGGCCCGGACGT[G/A]
GCGCTGATGGTAGCGCCGCAGGCTCTGCTGGTAGCGTGCGGCTCGGAGGGCCGCACGCCGCCTTCGTTCTTCCAAGTAGTCGAGGTCATCTCTACGAAGC
Reverse complement sequence
GCTTCGTAGAGATGACCTCGACTACTTGGAAGAACGAAGGCGGCGTGCGGCCCTCCGAGCCGCACGCTACCAGCAGAGCCTGCGGCGCTACCATCAGCGC[C/T]
ACGTCCGGGCCCGATCACTCTGCGTCGACGACCTCGTCTTACGCCGCGTTCAAACGCGTGCTGGATTGAGCAAGCTCTCACCAATGTGGGAGGGTCCGTA
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 | 37.30% | 0.30% | 4.95% | 57.43% | NA |
| All Indica | 2759 | 13.30% | 0.50% | 5.22% | 80.90% | NA |
| All Japonica | 1512 | 86.20% | 0.00% | 4.56% | 9.19% | NA |
| Aus | 269 | 3.70% | 0.00% | 0.00% | 96.28% | NA |
| Indica I | 595 | 35.50% | 0.30% | 2.52% | 61.68% | NA |
| Indica II | 465 | 4.30% | 0.20% | 2.58% | 92.90% | NA |
| Indica III | 913 | 4.90% | 1.10% | 7.78% | 86.20% | NA |
| Indica Intermediate | 786 | 11.70% | 0.30% | 5.85% | 82.19% | NA |
| Temperate Japonica | 767 | 92.30% | 0.00% | 4.43% | 3.26% | NA |
| Tropical Japonica | 504 | 85.10% | 0.00% | 2.78% | 12.10% | NA |
| Japonica Intermediate | 241 | 69.30% | 0.00% | 8.71% | 21.99% | NA |
| VI/Aromatic | 96 | 46.90% | 0.00% | 15.62% | 37.50% | NA |
| Intermediate | 90 | 40.00% | 0.00% | 6.67% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414145792 | G -> DEL | LOC_Os04g24640.1 | N | frameshift_variant | Average:16.389; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 | N | N | N | N |
| vg0414145792 | G -> A | LOC_Os04g24640.1 | missense_variant ; p.His438Tyr; MODERATE | nonsynonymous_codon ; H438Y | Average:16.389; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 | benign  |
0.179 |
DELETERIOUS | 0.00 |