Search for Variation information by Variation ID:
Detailed information for vg0112723984:
| Variant ID: vg0112723984 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723984 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCCGTGTAGGCGGAGGCACCACCCGGCGGCGACGGAGGCAGGCCGGCGGTGAAGTCGTAGACGCCCAACGGCGGCGGCATAATAGACCAGCCGTGTAGG[C/G]
GGAGGCACCAACCGGCGGCGACGGAGGCAAGCCGGTGGTGAAGACGTGGACGCCCATGAACGGTGGTGTGACCAACCAACCGTATAGGCGAAGACACCAG
Reverse complement sequence
CTGGTGTCTTCGCCTATACGGTTGGTTGGTCACACCACCGTTCATGGGCGTCCACGTCTTCACCACCGGCTTGCCTCCGTCGCCGCCGGTTGGTGCCTCC[G/C]
CCTACACGGCTGGTCTATTATGCCGCCGCCGTTGGGCGTCTACGACTTCACCGCCGGCCTGCCTCCGTCGCCGCCGGGTGGTGCCTCCGCCTACACGGCT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.70% | 0.10% | 26.39% | 41.83% | NA |
| All Indica | 2759 | 2.20% | 0.00% | 34.80% | 62.99% | NA |
| All Japonica | 1512 | 88.00% | 0.10% | 6.88% | 5.09% | NA |
| Aus | 269 | 4.80% | 0.00% | 46.10% | 49.07% | NA |
| Indica I | 595 | 1.70% | 0.00% | 14.45% | 83.87% | NA |
| Indica II | 465 | 4.30% | 0.00% | 23.66% | 72.04% | NA |
| Indica III | 913 | 0.90% | 0.00% | 56.41% | 42.72% | NA |
| Indica Intermediate | 786 | 2.80% | 0.10% | 31.68% | 65.39% | NA |
| Temperate Japonica | 767 | 94.70% | 0.00% | 2.61% | 2.74% | NA |
| Tropical Japonica | 504 | 80.40% | 0.00% | 9.92% | 9.72% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.40% | 14.11% | 2.90% | NA |
| VI/Aromatic | 96 | 51.00% | 4.20% | 39.58% | 5.21% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 23.33% | 27.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723984 | C -> G | LOC_Os01g22620.1 | missense_variant ; p.Ala149Pro; MODERATE | nonsynonymous_codon ; A149P | Average:24.843; most accessible tissue: Zhenshan97 root, score: 43.05 | probably damaging  |
2.406 |
DELETERIOUS | 0.00 |
| vg0112723984 | C -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:24.843; most accessible tissue: Zhenshan97 root, score: 43.05 | N | N | N | N |