Search for Variation information by Variation ID:
Detailed information for vg0602220614:
| Variant ID: vg0602220614 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 2220614 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACCACCGTGATGAACGAGGCGCAGGACACCCTCCGCCTTCAATACGGGAGCTGGGAGGCGGAGCTAGGGAAGAAGCTCGACGCCACCCAGGGGGTGCTTG[A/T]
CGCTGCCGCTGCCCGAGAACAGCGGGCGGCGGAGACCGAAGCGGCGTCCCGGCGGCGCGAAGAGGCCCTTGAGGCGCGCGCCATGGCGCTGGAAGAGCGC
Reverse complement sequence
GCGCTCTTCCAGCGCCATGGCGCGCGCCTCAAGGGCCTCTTCGCGCCGCCGGGACGCCGCTTCGGTCTCCGCCGCCCGCTGTTCTCGGGCAGCGGCAGCG[T/A]
CAAGCACCCCCTGGGTGGCGTCGAGCTTCTTCCCTAGCTCCGCCTCCCAGCTCCCGTATTGAAGGCGGAGGGTGTCCTGCGCCTCGTTCATCACGGTGGT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 0.90% | 0.50% | 12.21% | 86.39% | NA |
| All Indica | 2759 | 0.80% | 0.30% | 5.91% | 93.04% | NA |
| All Japonica | 1512 | 1.40% | 0.10% | 23.81% | 74.74% | NA |
| Aus | 269 | 0.00% | 3.30% | 10.41% | 86.25% | NA |
| Indica I | 595 | 0.00% | 0.00% | 1.68% | 98.32% | NA |
| Indica II | 465 | 1.90% | 0.00% | 12.04% | 86.02% | NA |
| Indica III | 913 | 0.70% | 0.20% | 5.15% | 93.98% | NA |
| Indica Intermediate | 786 | 0.80% | 0.80% | 6.36% | 92.11% | NA |
| Temperate Japonica | 767 | 1.60% | 0.00% | 15.78% | 82.66% | NA |
| Tropical Japonica | 504 | 1.60% | 0.20% | 35.32% | 62.90% | NA |
| Japonica Intermediate | 241 | 0.40% | 0.00% | 25.31% | 74.27% | NA |
| VI/Aromatic | 96 | 1.00% | 3.10% | 10.42% | 85.42% | NA |
| Intermediate | 90 | 1.10% | 1.10% | 17.78% | 80.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0602220614 | A -> T | LOC_Os06g05030.1 | missense_variant ; p.Asp716Val; MODERATE | nonsynonymous_codon ; D716V | Average:18.749; most accessible tissue: Minghui63 root, score: 50.524 | probably damaging  |
2.171 |
DELETERIOUS | 0.00 |
| vg0602220614 | A -> DEL | LOC_Os06g05030.1 | N | frameshift_variant | Average:18.749; most accessible tissue: Minghui63 root, score: 50.524 | N | N | N | N |