Search for Variation information by Variation ID:
Detailed information for vg0139513943:
| Variant ID: vg0139513943 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 39513943 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GTTTCTTTCCTCGATAACATCAAGCAGGCGTGGCAAATTGTCATATGAGGCTTTGTAAGTTCCAAATCTCATCTCTATTATTTTCTGTTTGGCCCTCCAG[G/A]
CCTTGGCATAGCTAATAGTATACTTGTATGTCTCTTCAATGTATCGGATTATTGACCTTGGTTCATATGTGAGATTATCGATGACATGCGCATACATCTC
Reverse complement sequence
GAGATGTATGCGCATGTCATCGATAATCTCACATATGAACCAAGGTCAATAATCCGATACATTGAAGAGACATACAAGTATACTATTAGCTATGCCAAGG[C/T]
CTGGAGGGCCAAACAGAAAATAATAGAGATGAGATTTGGAACTTACAAAGCCTCATATGACAATTTGCCACGCCTGCTTGATGTTATCGAGGAAAGAAAC
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 | 26.00% | 1.00% | 1.08% | 71.90% | NA |
| All Indica | 2759 | 2.50% | 0.40% | 1.41% | 95.65% | NA |
| All Japonica | 1512 | 74.30% | 0.30% | 0.13% | 25.26% | NA |
| Aus | 269 | 0.00% | 2.20% | 2.60% | 95.17% | NA |
| Indica I | 595 | 3.00% | 0.00% | 2.02% | 94.96% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.22% | 98.71% | NA |
| Indica III | 913 | 1.20% | 1.00% | 1.42% | 96.39% | NA |
| Indica Intermediate | 786 | 4.60% | 0.30% | 1.65% | 93.51% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.13% | 2.74% | NA |
| Tropical Japonica | 504 | 52.00% | 0.00% | 0.20% | 47.82% | NA |
| Japonica Intermediate | 241 | 48.50% | 1.70% | 0.00% | 49.79% | NA |
| VI/Aromatic | 96 | 1.00% | 22.90% | 1.04% | 75.00% | NA |
| Intermediate | 90 | 38.90% | 4.40% | 2.22% | 54.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0139513943 | G -> A | LOC_Os01g67990.1 | missense_variant ; p.Ala349Val; MODERATE | nonsynonymous_codon ; A349V | Average:7.208; most accessible tissue: Callus, score: 29.745 | benign  |
0.593 |
DELETERIOUS | 0.01 |
| vg0139513943 | G -> DEL | LOC_Os01g67990.1 | N | frameshift_variant | Average:7.208; most accessible tissue: Callus, score: 29.745 | N | N | N | N |