Search for Variation information by Variation ID:
Detailed information for vg1012224276:
| Variant ID: vg1012224276 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224276 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCAACGAGCCGGCGTGACGCCGAACGAGGTGACCCTCCTCGGCGTCCTCACGGCGTGCTGTCATGCCGGACTCATCGAGGAGGGGCTCCAGCAACTCGAC[G/A]
CCATGAGGAGGAACGAGATCGACAAGGTCCCCGGCTGCAGCCTCATCGAGATCGACGGCGTTGTGCACGAATTCAAAGCAATCCCAGCAAATTCCATCCG
Reverse complement sequence
CGGATGGAATTTGCTGGGATTGCTTTGAATTCGTGCACAACGCCGTCGATCTCGATGAGGCTGCAGCCGGGGACCTTGTCGATCTCGTTCCTCCTCATGG[C/T]
GTCGAGTTGCTGGAGCCCCTCCTCGATGAGTCCGGCATGACAGCACGCCGTGAGGACGCCGAGGAGGGTCACCTCGTTCGGCGTCACGCCGGCTCGTTGC
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 | 49.30% | 0.10% | 1.25% | 49.32% | NA |
| All Indica | 2759 | 31.80% | 0.10% | 1.81% | 66.22% | NA |
| All Japonica | 1512 | 89.80% | 0.00% | 0.07% | 10.12% | NA |
| Aus | 269 | 13.00% | 0.00% | 0.74% | 86.25% | NA |
| Indica I | 595 | 11.90% | 0.50% | 3.19% | 84.37% | NA |
| Indica II | 465 | 39.80% | 0.00% | 3.01% | 57.20% | NA |
| Indica III | 913 | 35.00% | 0.00% | 1.42% | 63.53% | NA |
| Indica Intermediate | 786 | 38.40% | 0.10% | 0.51% | 60.94% | NA |
| Temperate Japonica | 767 | 97.40% | 0.00% | 0.00% | 2.61% | NA |
| Tropical Japonica | 504 | 82.10% | 0.00% | 0.20% | 17.66% | NA |
| Japonica Intermediate | 241 | 81.70% | 0.00% | 0.00% | 18.26% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 3.12% | 89.58% | NA |
| Intermediate | 90 | 58.90% | 1.10% | 3.33% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224276 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Ala124Thr; MODERATE | nonsynonymous_codon ; A124T | Average:14.017; most accessible tissue: Callus, score: 56.934 | benign  |
0.118 |
TOLERATED | 0.41 |
| vg1012224276 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:14.017; most accessible tissue: Callus, score: 56.934 | N | N | N | N |