Search for Variation information by Variation ID:
Detailed information for vg0429946010:
| Variant ID: vg0429946010 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 29946010 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 300. )
Flanking Sequence (100 bp) in Reference Genome:
AAGCGAAAGGACAAAAAGAAAGGAGCTAGGACCTTTGGTCCGAGCTAACTAAAAGAAAGCCAGCTATTAAGACTTCTCGCTCCTGCTAAGGCCCAAGTTT[T/G]
GGCCTCTTCCTTGATCTTGGCTAAAAGAGAGATAGCTGAAAGCTCCTTCTGTTGGAAGGTTCTGCGATTCCTTTCGCTCCATATCTCCCAGGCGACCAAC
Reverse complement sequence
GTTGGTCGCCTGGGAGATATGGAGCGAAAGGAATCGCAGAACCTTCCAACAGAAGGAGCTTTCAGCTATCTCTCTTTTAGCCAAGATCAAGGAAGAGGCC[A/C]
AAACTTGGGCCTTAGCAGGAGCGAGAAGTCTTAATAGCTGGCTTTCTTTTAGTTAGCTCGGACCAAAGGTCCTAGCTCCTTTCTTTTTGTCCTTTCGCTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 92.40% | 7.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 34.40% | 65.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 8.90% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0429946010 | T -> G | LOC_Os04g50188.1 | missense_variant ; p.Lys94Gln; MODERATE | nonsynonymous_codon ; K94Q | Average:49.644; most accessible tissue: Minghui63 panicle, score: 62.157 | possibly damaging  |
1.702 |
TOLERATED | 0.47 |