Search for Variation information by Variation ID:
Detailed information for vg0137498663:
| Variant ID: vg0137498663 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37498663 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCTTCCCTAGCTCCGCCTCCCAGCTCCCGTATTAAAGGCGGAGGGTGTCCTGCGCCTCGTTCATCACGGTGGTGGCAATGAGGGCAGCCCCCCGCTCCT[C/T]
CTCTATTTCCTTGGCGATCTCCGCCAGCACCTTCTTACGAGTTTCAAGCTCCGAGACGTGCCGGCGGTGAGCCTTACGGCCCACCTCCACCATGGCCTCC
Reverse complement sequence
GGAGGCCATGGTGGAGGTGGGCCGTAAGGCTCACCGCCGGCACGTCTCGGAGCTTGAAACTCGTAAGAAGGTGCTGGCGGAGATCGCCAAGGAAATAGAG[G/A]
AGGAGCGGGGGGCTGCCCTCATTGCCACCACCGTGATGAACGAGGCGCAGGACACCCTCCGCCTTTAATACGGGAGCTGGGAGGCGGAGCTAGGGAAGAA
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 | 34.60% | 1.10% | 1.14% | 63.16% | NA |
| All Indica | 2759 | 2.40% | 0.00% | 1.45% | 96.12% | NA |
| All Japonica | 1512 | 93.70% | 3.30% | 0.93% | 2.05% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 1.20% | 0.00% | 1.34% | 97.48% | NA |
| Indica II | 465 | 1.50% | 0.00% | 1.94% | 96.56% | NA |
| Indica III | 913 | 1.10% | 0.00% | 0.88% | 98.03% | NA |
| Indica Intermediate | 786 | 5.50% | 0.00% | 1.91% | 92.62% | NA |
| Temperate Japonica | 767 | 90.20% | 6.30% | 1.83% | 1.69% | NA |
| Tropical Japonica | 504 | 97.40% | 0.00% | 0.00% | 2.58% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.80% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 0.00% | 35.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137498663 | C -> T | LOC_Os01g64610.1 | missense_variant ; p.Glu654Lys; MODERATE | nonsynonymous_codon ; E654K | Average:5.646; most accessible tissue: Callus, score: 13.478 | benign  |
0.278 |
DELETERIOUS | 0.00 |
| vg0137498663 | C -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:5.646; most accessible tissue: Callus, score: 13.478 | N | N | N | N |