Search for Variation information by Variation ID:
Detailed information for vg1212666314:
| Variant ID: vg1212666314 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666314 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 272. )
Flanking Sequence (100 bp) in Reference Genome:
ATGGATAACCGTAAAAGGAAAATGACTGTTTTCCAGGAGGCACAAGGTAGTAGCCAGAGGCAGCGTATCAAGCCACTCCAAATTGGTGAATCTTCTTCCG[C/T,A]
TGGTCAAGGACAGTCGCAACTGTTGAACATCGGTGGTGAGATCAAATTAGAGACTAATGAAAGTAATGAAGTAAACATCGAGCAAGCTAATCAGCCGGTG
Reverse complement sequence
CACCGGCTGATTAGCTTGCTCGATGTTTACTTCATTACTTTCATTAGTCTCTAATTTGATCTCACCACCGATGTTCAACAGTTGCGACTGTCCTTGACCA[G/A,T]
CGGAAGAAGATTCACCAATTTGGAGTGGCTTGATACGCTGCCTCTGGCTACTACCTTGTGCCTCCTGGAAAACAGTCATTTTCCTTTTACGGTTATCCAT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 80.90% | 0.60% | 0.95% | 17.54% | A: 0.06% |
| All Indica | 2759 | 82.30% | 0.90% | 0.94% | 15.84% | NA |
| All Japonica | 1512 | 75.70% | 0.10% | 0.79% | 23.35% | A: 0.07% |
| Aus | 269 | 95.50% | 0.00% | 0.74% | 3.72% | NA |
| Indica I | 595 | 70.30% | 0.30% | 0.50% | 28.91% | NA |
| Indica II | 465 | 79.80% | 2.60% | 1.94% | 15.70% | NA |
| Indica III | 913 | 91.20% | 0.30% | 0.55% | 7.89% | NA |
| Indica Intermediate | 786 | 82.60% | 1.00% | 1.15% | 15.27% | NA |
| Temperate Japonica | 767 | 84.50% | 0.30% | 0.13% | 15.12% | NA |
| Tropical Japonica | 504 | 69.00% | 0.00% | 1.98% | 28.77% | A: 0.20% |
| Japonica Intermediate | 241 | 61.40% | 0.00% | 0.41% | 38.17% | NA |
| VI/Aromatic | 96 | 84.40% | 0.00% | 3.12% | 10.42% | A: 2.08% |
| Intermediate | 90 | 76.70% | 0.00% | 2.22% | 21.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666314 | C -> DEL | LOC_Os12g22430.1 | N | frameshift_variant | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666314 | C -> A | LOC_Os12g22430.1 | missense_variant ; p.Ala260Asp; MODERATE | nonsynonymous_codon ; A260D | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | possibly damaging  |
1.912 |
DELETERIOUS | 0.01 |
| vg1212666314 | C -> T | LOC_Os12g22430.1 | missense_variant ; p.Ala260Val; MODERATE | nonsynonymous_codon ; A260V | Average:5.272; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign |
0.382 |
TOLERATED | 1.00 |