Search for Variation information by Variation ID:
Detailed information for vg0324793943:
| Variant ID: vg0324793943 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 24793943 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACTCCAAGCATTTTGTGTTCGAAAACCTGGCACGTCATGATCTGTTAGGAGCTCAATAAGGAACATCTTCATCTGGTGACTCCATCTGGCTCTCTTTGTC[G/A]
TCCCTAAATTTGACAAACATTTAACAATTTCAATTTCAGCAGCAATATGAAACAAAAAAGGTTTGATGCAAACAACAAGTGAAACTGAATTTGCAAATAT
Reverse complement sequence
ATATTTGCAAATTCAGTTTCACTTGTTGTTTGCATCAAACCTTTTTTGTTTCATATTGCTGCTGAAATTGAAATTGTTAAATGTTTGTCAAATTTAGGGA[C/T]
GACAAAGAGAGCCAGATGGAGTCACCAGATGAAGATGTTCCTTATTGAGCTCCTAACAGATCATGACGTGCCAGGTTTTCGAACACAAAATGCTTGGAGT
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 | 56.00% | 0.20% | 10.43% | 33.33% | NA |
| All Indica | 2759 | 34.70% | 0.00% | 12.69% | 52.59% | NA |
| All Japonica | 1512 | 98.70% | 0.70% | 0.07% | 0.60% | NA |
| Aus | 269 | 19.70% | 0.00% | 49.07% | 31.23% | NA |
| Indica I | 595 | 70.80% | 0.00% | 6.55% | 22.69% | NA |
| Indica II | 465 | 10.10% | 0.00% | 2.80% | 87.10% | NA |
| Indica III | 913 | 16.80% | 0.00% | 24.53% | 58.71% | NA |
| Indica Intermediate | 786 | 42.90% | 0.00% | 9.41% | 47.71% | NA |
| Temperate Japonica | 767 | 98.00% | 1.30% | 0.13% | 0.52% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 4.17% | 5.21% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 6.67% | 28.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324793943 | G -> A | LOC_Os03g44130.1 | missense_variant ; p.Thr47Met; MODERATE | nonsynonymous_codon ; T47M | Average:8.887; most accessible tissue: Zhenshan97 flower, score: 22.37 | probably damaging  |
2.447 |
TOLERATED | 0.07 |
| vg0324793943 | G -> DEL | LOC_Os03g44130.1 | N | frameshift_variant | Average:8.887; most accessible tissue: Zhenshan97 flower, score: 22.37 | N | N | N | N |