Search for Variation information by Variation ID:
Detailed information for vg0128477193:
| Variant ID: vg0128477193 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28477193 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 86. )
Flanking Sequence (100 bp) in Reference Genome:
ATGAAGCCTGGAATGTATCTGGCCGGGGCTGACGTGCCAACTCCAGGAGTTCCCACGCCGGCTCCGGCTAGGGACGAGTGCCTGGAGGCTCTCATCATTC[C/T]
GACGGGATGGGGCGAGGCGTGTGTCAGGCCGCCTGTTGCCCCCTAACCCGCGATCTGACCGGTCTGTGACCGGTCACACACTGCGACCGATCACGGACCG
Reverse complement sequence
CGGTCCGTGATCGGTCGCAGTGTGTGACCGGTCACAGACCGGTCAGATCGCGGGTTAGGGGGCAACAGGCGGCCTGACACACGCCTCGCCCCATCCCGTC[G/A]
GAATGATGAGAGCCTCCAGGCACTCGTCCCTAGCCGGAGCCGGCGTGGGAACTCCTGGAGTTGGCACGTCAGCCCCGGCCAGATACATTCCAGGCTTCAT
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 | 30.30% | 0.20% | 0.72% | 68.81% | NA |
| All Indica | 2759 | 1.90% | 0.30% | 0.36% | 97.46% | NA |
| All Japonica | 1512 | 87.50% | 0.10% | 0.73% | 11.71% | NA |
| Aus | 269 | 1.10% | 0.00% | 3.35% | 95.54% | NA |
| Indica I | 595 | 1.20% | 1.30% | 0.84% | 96.64% | NA |
| Indica II | 465 | 3.90% | 0.00% | 0.00% | 96.13% | NA |
| Indica III | 913 | 0.80% | 0.00% | 0.22% | 99.01% | NA |
| Indica Intermediate | 786 | 2.50% | 0.00% | 0.38% | 97.07% | NA |
| Temperate Japonica | 767 | 94.90% | 0.10% | 0.91% | 4.04% | NA |
| Tropical Japonica | 504 | 73.60% | 0.00% | 0.60% | 25.79% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.00% | 0.41% | 6.64% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 1.04% | 85.42% | NA |
| Intermediate | 90 | 44.40% | 0.00% | 3.33% | 52.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128477193 | C -> T | LOC_Os01g49500.1 | missense_variant ; p.Pro94Leu; MODERATE | nonsynonymous_codon ; P94L | Average:5.814; most accessible tissue: Callus, score: 15.328 | probably damaging  |
2.029 |
DELETERIOUS | 0.04 |
| vg0128477193 | C -> DEL | LOC_Os01g49500.1 | N | frameshift_variant | Average:5.814; most accessible tissue: Callus, score: 15.328 | N | N | N | N |