Search for Variation information by Variation ID:
Detailed information for vg1212666378:
| Variant ID: vg1212666378 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666378 |
| Reference Allele: T | Alternative Allele: A,C |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAG[T/A,C]
AATGAAGTAAACATCGAGCAAGCTAATCAGCCGGTGCCAGTTCAGCAGGATCAGTCTCAGGAGAATAACAGTAGTGGAAGGGAGCAGTAGGTATGTTTCA
Reverse complement sequence
TGAAACATACCTACTGCTCCCTTCCACTACTGTTATTCTCCTGAGACTGATCCTGCTGAACTGGCACCGGCTGATTAGCTTGCTCGATGTTTACTTCATT[A/T,G]
CTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATAC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 16.70% | 0.80% | 14.49% | 67.84% | C: 0.13% |
| All Indica | 2759 | 3.80% | 1.20% | 21.02% | 73.76% | C: 0.22% |
| All Japonica | 1512 | 43.20% | 0.40% | 1.12% | 55.29% | NA |
| Aus | 269 | 3.00% | 0.00% | 27.14% | 69.89% | NA |
| Indica I | 595 | 1.00% | 1.50% | 11.43% | 85.88% | C: 0.17% |
| Indica II | 465 | 3.00% | 0.90% | 25.81% | 70.11% | C: 0.22% |
| Indica III | 913 | 4.20% | 1.50% | 25.52% | 68.57% | C: 0.22% |
| Indica Intermediate | 786 | 6.00% | 0.80% | 20.23% | 72.77% | C: 0.25% |
| Temperate Japonica | 767 | 77.10% | 0.00% | 0.78% | 22.16% | NA |
| Tropical Japonica | 504 | 1.40% | 1.00% | 1.59% | 96.03% | NA |
| Japonica Intermediate | 241 | 22.80% | 0.40% | 1.24% | 75.52% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 5.21% | 94.79% | NA |
| Intermediate | 90 | 25.60% | 1.10% | 11.11% | 62.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666378 | T -> C | LOC_Os12g22430.1 | synonymous_variant ; p.Ser281Ser; LOW | synonymous_codon | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666378 | T -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666378 | T -> A | LOC_Os12g22430.1 | missense_variant ; p.Ser281Arg; MODERATE | nonsynonymous_codon ; S281R | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | possibly damaging  |
1.871 |
DELETERIOUS | 0.02 |