Search for Variation information by Variation ID:
Detailed information for vg1212666387:
| Variant ID: vg1212666387 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666387 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, A: 0.23, others allele: 0.00, population size: 82. )
Flanking Sequence (100 bp) in Reference Genome:
CACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGT[A/T]
AACATCGAGCAAGCTAATCAGCCGGTGCCAGTTCAGCAGGATCAGTCTCAGGAGAATAACAGTAGTGGAAGGGAGCAGTAGGTATGTTTCAACTGTTACA
Reverse complement sequence
TGTAACAGTTGAAACATACCTACTGCTCCCTTCCACTACTGTTATTCTCCTGAGACTGATCCTGCTGAACTGGCACCGGCTGATTAGCTTGCTCGATGTT[T/A]
ACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTG
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 | 16.30% | 1.00% | 12.12% | 70.59% | NA |
| All Indica | 2759 | 3.40% | 1.40% | 17.69% | 77.42% | NA |
| All Japonica | 1512 | 43.20% | 0.20% | 0.79% | 55.82% | NA |
| Aus | 269 | 0.00% | 1.50% | 23.42% | 75.09% | NA |
| Indica I | 595 | 1.00% | 1.20% | 6.72% | 91.09% | NA |
| Indica II | 465 | 2.80% | 1.50% | 22.80% | 72.90% | NA |
| Indica III | 913 | 3.60% | 2.10% | 22.23% | 72.07% | NA |
| Indica Intermediate | 786 | 5.50% | 0.90% | 17.68% | 75.95% | NA |
| Temperate Japonica | 767 | 77.10% | 0.00% | 0.52% | 22.43% | NA |
| Tropical Japonica | 504 | 1.40% | 0.60% | 0.99% | 97.02% | NA |
| Japonica Intermediate | 241 | 22.80% | 0.00% | 1.24% | 75.93% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 7.78% | 67.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666387 | A -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666387 | A -> T | LOC_Os12g22430.1 | synonymous_variant ; p.Val284Val; LOW | synonymous_codon | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666387 | A -> T | LOC_Os12g22430.1 | synonymous_variant ; p.Val284Val; LOW | nonsynonymous_codon ; V284I | Average:5.218; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
1.068 |
TOLERATED | 1.00 |