Search for Variation information by Variation ID:
Detailed information for vg1212666332:
| Variant ID: vg1212666332 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666332 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGC[A/G]
ACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTAAACATCGAGCAAGCTAATCAGCCGGTGCCAGTTCAGCAGGATCAG
Reverse complement sequence
CTGATCCTGCTGAACTGGCACCGGCTGATTAGCTTGCTCGATGTTTACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGT[T/C]
GCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTT
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 | 81.10% | 0.50% | 1.12% | 17.22% | NA |
| All Indica | 2759 | 82.60% | 0.80% | 1.30% | 15.30% | NA |
| All Japonica | 1512 | 75.80% | 0.10% | 0.79% | 23.35% | NA |
| Aus | 269 | 95.50% | 0.00% | 0.37% | 4.09% | NA |
| Indica I | 595 | 70.60% | 0.50% | 1.68% | 27.23% | NA |
| Indica II | 465 | 80.40% | 2.80% | 1.08% | 15.70% | NA |
| Indica III | 913 | 91.50% | 0.00% | 0.77% | 7.78% | NA |
| Indica Intermediate | 786 | 82.60% | 0.90% | 1.78% | 14.76% | NA |
| Temperate Japonica | 767 | 84.60% | 0.10% | 0.13% | 15.12% | NA |
| Tropical Japonica | 504 | 69.20% | 0.00% | 1.98% | 28.77% | NA |
| Japonica Intermediate | 241 | 61.40% | 0.00% | 0.41% | 38.17% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 2.08% | 10.42% | NA |
| Intermediate | 90 | 77.80% | 0.00% | 2.22% | 20.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666332 | A -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666332 | A -> G | LOC_Os12g22430.1 | missense_variant ; p.Gln266Arg; MODERATE | nonsynonymous_codon ; Q266R | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
1.241 |
TOLERATED | 0.06 |