Search for Variation information by Variation ID:
Detailed information for vg0409586830:
| Variant ID: vg0409586830 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586830 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TATGCAGATTCGGTGGCCGTTTGAAGTCAGCAGTGTAGTAGGTGGCCGAATCGGATTCCAGCACTTGGAGTACTTGATCTCGATATCTTCTTGTTCATCC[A/T]
TGATGTGAGCAATGGTTGCATCCGTGGTAGCCATGGTCACATCAATAGGTAAATCCTATGTGTAACATATAATAATCTTGGTTGATGATATATAATTTCA
Reverse complement sequence
TGAAATTATATATCATCAACCAAGATTATTATATGTTACACATAGGATTTACCTATTGATGTGACCATGGCTACCACGGATGCAACCATTGCTCACATCA[T/A]
GGATGAACAAGAAGATATCGAGATCAAGTACTCCAAGTGCTGGAATCCGATTCGGCCACCTACTACACTGCTGACTTCAAACGGCCACCGAATCTGCATA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 23.10% | 0.60% | 7.47% | 68.85% | NA |
| All Indica | 2759 | 4.90% | 0.90% | 8.01% | 86.23% | NA |
| All Japonica | 1512 | 61.10% | 0.10% | 7.28% | 31.48% | NA |
| Aus | 269 | 3.00% | 0.00% | 0.00% | 97.03% | NA |
| Indica I | 595 | 8.20% | 0.70% | 6.89% | 84.20% | NA |
| Indica II | 465 | 6.70% | 0.90% | 6.88% | 85.59% | NA |
| Indica III | 913 | 0.90% | 1.30% | 7.34% | 90.47% | NA |
| Indica Intermediate | 786 | 6.00% | 0.50% | 10.31% | 83.21% | NA |
| Temperate Japonica | 767 | 96.10% | 0.00% | 0.78% | 3.13% | NA |
| Tropical Japonica | 504 | 4.20% | 0.20% | 15.28% | 80.36% | NA |
| Japonica Intermediate | 241 | 68.90% | 0.40% | 11.20% | 19.50% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 16.67% | 83.33% | NA |
| Intermediate | 90 | 27.80% | 1.10% | 6.67% | 64.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586830 | A -> DEL | LOC_Os04g17520.1 | N | frameshift_variant | Average:15.542; most accessible tissue: Minghui63 root, score: 27.443 | N | N | N | N |
| vg0409586830 | A -> T | LOC_Os04g17520.1 | missense_variant ; p.Met12Lys; MODERATE | nonsynonymous_codon ; M12K | Average:15.542; most accessible tissue: Minghui63 root, score: 27.443 | benign  |
1.303 |
DELETERIOUS | 0.00 |