Search for Variation information by Variation ID:
Detailed information for vg0112723183:
| Variant ID: vg0112723183 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723183 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CATCAATAACAATGAAGACACCAGTCGGCGGCGACGAAGGCGGTCGACGGTGAAAGCGAAGATGCCCACTAATGGCGGCATAATAGGTCAGCCGTGTAAG[C/T]
GGAAACACCAGTCGACGGCAACGAAGGTGAGCCAACGGTGACGATGTAGACATCCAACAACGGCGGCATAATAGGCCAGCCGTGTAGGAGGAGGCACCAC
Reverse complement sequence
GTGGTGCCTCCTCCTACACGGCTGGCCTATTATGCCGCCGTTGTTGGATGTCTACATCGTCACCGTTGGCTCACCTTCGTTGCCGTCGACTGGTGTTTCC[G/A]
CTTACACGGCTGACCTATTATGCCGCCATTAGTGGGCATCTTCGCTTTCACCGTCGACCGCCTTCGTCGCCGCCGACTGGTGTCTTCATTGTTATTGATG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 42.80% | 0.50% | 17.94% | 38.79% | NA |
| All Indica | 2759 | 16.10% | 0.00% | 24.03% | 59.84% | NA |
| All Japonica | 1512 | 88.00% | 1.20% | 8.99% | 1.79% | NA |
| Aus | 269 | 49.80% | 0.00% | 5.95% | 44.24% | NA |
| Indica I | 595 | 3.40% | 0.00% | 7.90% | 88.74% | NA |
| Indica II | 465 | 13.10% | 0.00% | 34.62% | 52.26% | NA |
| Indica III | 913 | 24.80% | 0.00% | 31.76% | 43.48% | NA |
| Indica Intermediate | 786 | 17.60% | 0.00% | 20.99% | 61.45% | NA |
| Temperate Japonica | 767 | 94.80% | 0.10% | 4.30% | 0.78% | NA |
| Tropical Japonica | 504 | 80.20% | 3.00% | 13.49% | 3.37% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.80% | 14.52% | 1.66% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 19.79% | 16.67% | NA |
| Intermediate | 90 | 57.80% | 4.40% | 15.56% | 22.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723183 | C -> T | LOC_Os01g22620.1 | missense_variant ; p.Ala416Thr; MODERATE | nonsynonymous_codon ; A416T | Average:16.754; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | benign  |
1.244 |
DELETERIOUS | 0.04 |
| vg0112723183 | C -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:16.754; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | N | N | N | N |