Search for Variation information by Variation ID:
Detailed information for vg0221508931:
| Variant ID: vg0221508931 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21508931 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCGATGGGGAAGGGCGGCGAGATGGGGAGCGTCGCCTCCTCGTCTACGGTGACGGCAGCACGCCCCAGGGCGCGCTCCAAGCTGCGGGCGCGCTCCTAC[G/A]
TCACCCGCCCGTTGTCCCTGACCCGGAGTCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACTTGGTCATGACGGCACGGCAGCGCCTAGGTGCTGGT
Reverse complement sequence
ACCAGCACCTAGGCGCTGCCGTGCCGTCATGACCAAGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGACTCCGGGTCAGGGACAACGGGCGGGTGA[C/T]
GTAGGAGCGCGCCCGCAGCTTGGAGCGCGCCCTGGGGCGTGCTGCCGTCACCGTAGACGAGGAGGCGACGCTCCCCATCTCGCCGCCCTTCCCCATCGCC
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 | 36.30% | 0.50% | 2.98% | 60.20% | NA |
| All Indica | 2759 | 5.00% | 0.00% | 4.35% | 90.61% | NA |
| All Japonica | 1512 | 94.60% | 1.60% | 0.73% | 3.11% | NA |
| Aus | 269 | 2.20% | 0.00% | 1.12% | 96.65% | NA |
| Indica I | 595 | 3.00% | 0.00% | 2.35% | 94.62% | NA |
| Indica II | 465 | 5.80% | 0.00% | 9.46% | 84.73% | NA |
| Indica III | 913 | 5.00% | 0.00% | 3.29% | 91.68% | NA |
| Indica Intermediate | 786 | 6.10% | 0.00% | 4.07% | 89.82% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.26% | 1.04% | NA |
| Tropical Japonica | 504 | 87.10% | 4.80% | 1.19% | 6.94% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 1.24% | 1.66% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 57.80% | 0.00% | 7.78% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0221508931 | G -> A | LOC_Os02g35800.1 | missense_variant ; p.Arg90His; MODERATE | nonsynonymous_codon ; R90H | Average:11.107; most accessible tissue: Callus, score: 25.55 | benign  |
0.427 |
DELETERIOUS | 0.03 |
| vg0221508931 | G -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:11.107; most accessible tissue: Callus, score: 25.55 | N | N | N | N |