Search for Variation information by Variation ID:
Detailed information for vg0206046813:
| Variant ID: vg0206046813 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 6046813 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CAGCGCCGTGGACGTCGTACCTCCAGCTGGTCCGGTACAACCACGGCCTCACGCGCCTACCGTCGGAGCAGGACCTCGACCTACGGCACCTGTTTCGCAC[G/A]
GTACTGCTCAGCCCAGAGGTTTCTTAAGTTTTGTTTATGTTTTTGTACGAAAACATCACCCCGTCGTAACTTGATGTTCCATCCTCACAGGACCTCGTTT
Reverse complement sequence
AAACGAGGTCCTGTGAGGATGGAACATCAAGTTACGACGGGGTGATGTTTTCGTACAAAAACATAAACAAAACTTAAGAAACCTCTGGGCTGAGCAGTAC[C/T]
GTGCGAAACAGGTGCCGTAGGTCGAGGTCCTGCTCCGACGGTAGGCGCGTGAGGCCGTGGTTGTACCGGACCAGCTGGAGGTACGACGTCCACGGCGCTG
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.30% | 0.10% | 6.86% | 59.67% | NA |
| All Indica | 2759 | 1.60% | 0.00% | 8.59% | 89.85% | NA |
| All Japonica | 1512 | 96.60% | 0.10% | 0.99% | 2.38% | NA |
| Aus | 269 | 1.50% | 0.00% | 18.22% | 80.30% | NA |
| Indica I | 595 | 1.00% | 0.00% | 6.39% | 92.61% | NA |
| Indica II | 465 | 2.60% | 0.00% | 15.05% | 82.37% | NA |
| Indica III | 913 | 1.20% | 0.00% | 8.11% | 90.69% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 7.00% | 91.22% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.39% | 2.09% | NA |
| Tropical Japonica | 504 | 95.80% | 0.20% | 1.59% | 2.38% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 1.66% | 3.32% | NA |
| VI/Aromatic | 96 | 33.30% | 4.20% | 15.62% | 46.88% | NA |
| Intermediate | 90 | 40.00% | 2.20% | 8.89% | 48.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0206046813 | G -> A | LOC_Os02g11730.1 | missense_variant&splice_region_variant ; p.Gly1434Arg; MODERATE | nonsynonymous_codon ; G1434R | Average:11.219; most accessible tissue: Callus, score: 26.2 | probably damaging  |
2.607 |
DELETERIOUS | 0.04 |
| vg0206046813 | G -> DEL | LOC_Os02g11730.1 | N | frameshift_variant | Average:11.219; most accessible tissue: Callus, score: 26.2 | N | N | N | N |