Search for Variation information by Variation ID:
Detailed information for vg0409515146:
| Variant ID: vg0409515146 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515146 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTAAAACACATCGGCTGTCATGCATCAGCAACACTAGCCGATCATGCGTCAACCCAAACACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCC[A/G]
TCCATAAACCTCACCATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCG
Reverse complement sequence
CGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATGGTGAGGTTTATGGA[T/C]
GGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGTGTTTGGGTTGACGCATGATCGGCTAGTGTTGCTGATGCATGACAGCCGATGTGTTTTAC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.80% | 0.10% | 0.28% | 8.89% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.00% | 0.04% | NA |
| All Japonica | 1512 | 73.30% | 0.10% | 0.60% | 26.06% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 31.50% | 0.00% | 1.39% | 67.06% | NA |
| Japonica Intermediate | 241 | 80.10% | 0.40% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 71.90% | 1.00% | 2.08% | 25.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 2.22% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515146 | A -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:36.962; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg0409515146 | A -> G | LOC_Os04g17380.1 | missense_variant ; p.Trp154Arg; MODERATE | nonsynonymous_codon ; W154R | Average:36.962; most accessible tissue: Minghui63 young leaf, score: 61.887 | probably damaging  |
-3.548 |
TOLERATED | 1.00 |