Search for Variation information by Variation ID:
Detailed information for vg0629062192:
| Variant ID: vg0629062192 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 29062192 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, G: 0.08, others allele: 0.00, population size: 295. )
Flanking Sequence (100 bp) in Reference Genome:
CACAATTCTTCTTTACCCTTCTGCTGACGTGATTTAGATCTCAAAGCAGCATTTCTGACTACAGAACCAATTGCATGTGCAGACACCCCTGAAGAAACAG[A/G]
AGAATCTAATAGTTCAGGATCAAGTTCTGCAGGCTGATCTTCAGTAGTTGATGTGGACAACAAATCTTCTGGCTCATCCTGCTGACCATATGGATGCACA
Reverse complement sequence
TGTGCATCCATATGGTCAGCAGGATGAGCCAGAAGATTTGTTGTCCACATCAACTACTGAAGATCAGCCTGCAGAACTTGATCCTGAACTATTAGATTCT[T/C]
CTGTTTCTTCAGGGGTGTCTGCACATGCAATTGGTTCTGTAGTCAGAAATGCTGCTTTGAGATCTAAATCACGTCAGCAGAAGGGTAAAGAAGAATTGTG
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 | 61.30% | 38.20% | 0.00% | 0.47% | NA |
| All Indica | 2759 | 37.70% | 61.60% | 0.00% | 0.69% | NA |
| All Japonica | 1512 | 97.60% | 2.20% | 0.00% | 0.13% | NA |
| Aus | 269 | 84.80% | 15.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 62.90% | 36.00% | 0.00% | 1.18% | NA |
| Indica II | 465 | 40.20% | 59.10% | 0.00% | 0.65% | NA |
| Indica III | 913 | 20.60% | 78.90% | 0.00% | 0.55% | NA |
| Indica Intermediate | 786 | 37.00% | 62.50% | 0.00% | 0.51% | NA |
| Temperate Japonica | 767 | 99.00% | 0.90% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.90% | 1.70% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 28.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0629062192 | A -> G | LOC_Os06g48040.1 | missense_variant ; p.Ser151Pro; MODERATE | nonsynonymous_codon ; S151P | Average:73.92; most accessible tissue: Minghui63 flower, score: 82.891 | benign  |
-0.173 |
TOLERATED | 0.25 |
| vg0629062192 | A -> DEL | LOC_Os06g48040.1 | N | frameshift_variant | Average:73.92; most accessible tissue: Minghui63 flower, score: 82.891 | N | N | N | N |