Search for Variation information by Variation ID:
Detailed information for vg0410565223:
| Variant ID: vg0410565223 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10565223 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AATCTCTGCCAACCAACAACTTTCCAAATAGCACGAAAATCAACATCCATACCTATCTTTTTCAGCAGCTCCGGAGAGTATTCTCGTGTGTGAGCATACT[C/T]
CCGGTCACTCAGCATGTAGTAGGCTTGTCTTTCCCGATCGTCGACAAGGTCGAGGTCGGCGTCATTCAAGAGACGTCGTGGAGCTTCGGCATCCTCCATC
Reverse complement sequence
GATGGAGGATGCCGAAGCTCCACGACGTCTCTTGAATGACGCCGACCTCGACCTTGTCGACGATCGGGAAAGACAAGCCTACTACATGCTGAGTGACCGG[G/A]
AGTATGCTCACACACGAGAATACTCTCCGGAGCTGCTGAAAAAGATAGGTATGGATGTTGATTTTCGTGCTATTTGGAAAGTTGTTGGTTGGCAGAGATT
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 | 40.40% | 0.10% | 0.66% | 58.89% | NA |
| All Indica | 2759 | 9.00% | 0.10% | 1.01% | 89.89% | NA |
| All Japonica | 1512 | 99.30% | 0.10% | 0.00% | 0.66% | NA |
| Aus | 269 | 5.90% | 0.00% | 0.00% | 94.05% | NA |
| Indica I | 595 | 5.00% | 0.00% | 1.18% | 93.78% | NA |
| Indica II | 465 | 26.20% | 0.00% | 0.86% | 72.90% | NA |
| Indica III | 913 | 1.80% | 0.40% | 0.88% | 96.93% | NA |
| Indica Intermediate | 786 | 10.10% | 0.00% | 1.15% | 88.80% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 98.80% | 0.20% | 0.00% | 0.99% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 2.22% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410565223 | C -> DEL | LOC_Os04g19010.1 | N | frameshift_variant | Average:9.77; most accessible tissue: Callus, score: 40.877 | N | N | N | N |
| vg0410565223 | C -> T | LOC_Os04g19010.1 | missense_variant ; p.Glu34Lys; MODERATE | nonsynonymous_codon ; E34K | Average:9.77; most accessible tissue: Callus, score: 40.877 | benign  |
0.553 |
DELETERIOUS | 0.04 |