Search for Variation information by Variation ID:
Detailed information for vg0414146540:
| Variant ID: vg0414146540 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 14146540 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 186. )
Flanking Sequence (100 bp) in Reference Genome:
GCCATGAAAGTGGTATGATCTGCAGGGCCTGGGCCGGCTGATGGATTTGCTTGGCGTGGAACTGACACGCTCTGCATCGCCGAACCAGGTCGACCGCGTC[A/C]
TTGAGGGCAGTCGGCCAATAGAATCCTTGACGAAAGGCCTTGCCAACCAGGGTGCGCGAGGCAGAATGGGCTCCGCACTCGCCTTCATGGATATCGGCAA
Reverse complement sequence
TTGCCGATATCCATGAAGGCGAGTGCGGAGCCCATTCTGCCTCGCGCACCCTGGTTGGCAAGGCCTTTCGTCAAGGATTCTATTGGCCGACTGCCCTCAA[T/G]
GACGCGGTCGACCTGGTTCGGCGATGCAGAGCGTGTCAGTTCCACGCCAAGCAAATCCATCAGCCGGCCCAGGCCCTGCAGATCATACCACTTTCATGGC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 6.40% | 0.20% | 17.94% | 75.45% | NA |
| All Indica | 2759 | 2.60% | 0.00% | 5.26% | 92.13% | NA |
| All Japonica | 1512 | 14.90% | 0.00% | 44.51% | 40.54% | NA |
| Aus | 269 | 0.70% | 0.00% | 2.60% | 96.65% | NA |
| Indica I | 595 | 7.20% | 0.00% | 16.30% | 76.47% | NA |
| Indica II | 465 | 0.90% | 0.00% | 1.51% | 97.63% | NA |
| Indica III | 913 | 1.30% | 0.00% | 1.10% | 97.59% | NA |
| Indica Intermediate | 786 | 1.70% | 0.00% | 3.94% | 94.40% | NA |
| Temperate Japonica | 767 | 28.00% | 0.00% | 37.29% | 34.68% | NA |
| Tropical Japonica | 504 | 0.60% | 0.00% | 58.53% | 40.87% | NA |
| Japonica Intermediate | 241 | 3.30% | 0.00% | 38.17% | 58.51% | NA |
| VI/Aromatic | 96 | 1.00% | 9.40% | 8.33% | 81.25% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 16.67% | 81.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0414146540 | A -> C | LOC_Os04g24640.1 | missense_variant ; p.Asn188Lys; MODERATE | nonsynonymous_codon | Average:4.793; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | possibly damaging  |
1.652 |
DELETERIOUS | 0.00 |
| vg0414146540 | A -> DEL | LOC_Os04g24640.1 | N | frameshift_variant | Average:4.793; most accessible tissue: Zhenshan97 flag leaf, score: 7.948 | N | N | N | N |