Search for Variation information by Variation ID:
Detailed information for vg0409515160:
| Variant ID: vg0409515160 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515160 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTGTCATGCATCAGCAACACTAGCCGATCATGCGTCAACCCAAACACTTGGGTAATACTTCTTCAAGTATTTGCCATTGAGCGCCCATCCATAAACCTCA[C/A]
CATCAAGCCCTTGCAACATATATGCCCCTTTAGACACAACATTATAGATTTGAAACGGTCCTTCCCAATTTGGTGACCACTTGCCGAACTTGTTATCCCG
Reverse complement sequence
CGGGATAACAAGTTCGGCAAGTGGTCACCAAATTGGGAAGGACCGTTTCAAATCTATAATGTTGTGTCTAAAGGGGCATATATGTTGCAAGGGCTTGATG[G/T]
TGAGGTTTATGGATGGGCGCTCAATGGCAAATACTTGAAGAAGTATTACCCAAGTGTTTGGGTTGACGCATGATCGGCTAGTGTTGCTGATGCATGACAG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.90% | 0.00% | 0.30% | 8.80% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.04% | 0.04% | NA |
| All Japonica | 1512 | 73.50% | 0.00% | 0.79% | 25.73% | 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 | 99.40% | 0.20% | 0.22% | 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 | 31.90% | 0.00% | 1.98% | 66.07% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 0.83% | 18.67% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 1.04% | 26.04% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515160 | C -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:35.228; most accessible tissue: Minghui63 young leaf, score: 61.887 | N | N | N | N |
| vg0409515160 | C -> A | LOC_Os04g17380.1 | missense_variant ; p.Gly149Val; MODERATE | nonsynonymous_codon ; G149V | Average:35.228; most accessible tissue: Minghui63 young leaf, score: 61.887 | probably damaging  |
2.335 |
DELETERIOUS | 0.01 |