Search for Variation information by Variation ID:
Detailed information for vg0112723225:
| Variant ID: vg0112723225 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 12723225 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTCGACGGTGAAAGCGAAGATGCCCACTAATGGCGGCATAATAGGTCAGCCGTGTAAGCGGAAACACCAGTCGACGGCAACGAAGGTGAGCCAACGGTGA[C/G]
GATGTAGACATCCAACAACGGCGGCATAATAGGCCAGCCGTGTAGGAGGAGGCACCACTCGGCGGCGACGGAGGCAGGCCGGCGGTGAAGTCGTAGACGC
Reverse complement sequence
GCGTCTACGACTTCACCGCCGGCCTGCCTCCGTCGCCGCCGAGTGGTGCCTCCTCCTACACGGCTGGCCTATTATGCCGCCGTTGTTGGATGTCTACATC[G/C]
TCACCGTTGGCTCACCTTCGTTGCCGTCGACTGGTGTTTCCGCTTACACGGCTGACCTATTATGCCGCCATTAGTGGGCATCTTCGCTTTCACCGTCGAC
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 | 55.40% | 0.10% | 12.78% | 31.65% | NA |
| All Indica | 2759 | 29.60% | 0.20% | 20.51% | 49.66% | NA |
| All Japonica | 1512 | 97.40% | 0.00% | 0.99% | 1.59% | NA |
| Aus | 269 | 63.20% | 0.00% | 5.95% | 30.86% | NA |
| Indica I | 595 | 16.30% | 0.00% | 5.55% | 78.15% | NA |
| Indica II | 465 | 23.00% | 0.00% | 33.76% | 43.23% | NA |
| Indica III | 913 | 41.80% | 0.50% | 25.52% | 32.09% | NA |
| Indica Intermediate | 786 | 29.50% | 0.00% | 18.19% | 52.29% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 94.00% | 0.00% | 2.98% | 2.98% | NA |
| Japonica Intermediate | 241 | 98.30% | 0.00% | 0.00% | 1.66% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 73.30% | 1.10% | 7.78% | 17.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723225 | C -> G | LOC_Os01g22620.1 | missense_variant ; p.Val402Leu; MODERATE | nonsynonymous_codon ; V402L | Average:16.97; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | benign  |
-1.115 |
DELETERIOUS | 0.04 |
| vg0112723225 | C -> DEL | LOC_Os01g22620.1 | N | frameshift_variant | Average:16.97; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 | N | N | N | N |