Search for Variation information by Variation ID:
Detailed information for vg1212666377:
| Variant ID: vg1212666377 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666377 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCGCTGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAA[G/T]
TAATGAAGTAAACATCGAGCAAGCTAATCAGCCGGTGCCAGTTCAGCAGGATCAGTCTCAGGAGAATAACAGTAGTGGAAGGGAGCAGTAGGTATGTTTC
Reverse complement sequence
GAAACATACCTACTGCTCCCTTCCACTACTGTTATTCTCCTGAGACTGATCCTGCTGAACTGGCACCGGCTGATTAGCTTGCTCGATGTTTACTTCATTA[C/A]
TTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCAGCGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 16.90% | 0.20% | 19.68% | 63.14% | NA |
| All Indica | 2759 | 4.00% | 0.00% | 27.26% | 68.72% | NA |
| All Japonica | 1512 | 43.70% | 0.00% | 0.86% | 55.42% | NA |
| Aus | 269 | 1.10% | 4.10% | 47.96% | 46.84% | NA |
| Indica I | 595 | 1.20% | 0.00% | 8.91% | 89.92% | NA |
| Indica II | 465 | 3.20% | 0.00% | 21.51% | 75.27% | NA |
| Indica III | 913 | 4.50% | 0.00% | 44.69% | 50.82% | NA |
| Indica Intermediate | 786 | 6.10% | 0.00% | 24.30% | 69.59% | NA |
| Temperate Japonica | 767 | 77.20% | 0.00% | 0.65% | 22.16% | NA |
| Tropical Japonica | 504 | 2.60% | 0.00% | 0.99% | 96.43% | NA |
| Japonica Intermediate | 241 | 23.20% | 0.00% | 1.24% | 75.52% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 25.00% | 73.96% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 13.33% | 58.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666377 | G -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666377 | G -> T | LOC_Os12g22430.1 | missense_variant ; p.Ser281Ile; MODERATE | nonsynonymous_codon ; S281I | Average:5.035; most accessible tissue: Zhenshan97 panicle, score: 16.188 | possibly damaging  |
1.948 |
DELETERIOUS | 0.00 |