Search for Variation information by Variation ID:
Detailed information for vg0125111760:
| Variant ID: vg0125111760 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25111760 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGCGCAGCGCACGCTTATCCGGTCCGTGACCGGTCGCAGTGTGTGACCGGTCAGATCGCGGGTTAGGTGGCAACAGGCGGCCTGTCACACGCCTCGCCCC[G/A]
TCCCATCGAAATGATGAGAGCCTCCATGCTCTCGTCCCTAGCCGGAGCCGGCGTGTTAACTCCTGGAGTTGGCACGTCAGTCCCGGCCAGATACATTCCA
Reverse complement sequence
TGGAATGTATCTGGCCGGGACTGACGTGCCAACTCCAGGAGTTAACACGCCGGCTCCGGCTAGGGACGAGAGCATGGAGGCTCTCATCATTTCGATGGGA[C/T]
GGGGCGAGGCGTGTGACAGGCCGCCTGTTGCCACCTAACCCGCGATCTGACCGGTCACACACTGCGACCGGTCACGGACCGGATAAGCGTGCGCTGCGCT
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 | 17.60% | 1.00% | 3.81% | 77.59% | NA |
| All Indica | 2759 | 1.10% | 1.60% | 5.22% | 92.06% | NA |
| All Japonica | 1512 | 49.70% | 0.00% | 0.20% | 50.07% | NA |
| Aus | 269 | 2.60% | 0.00% | 10.04% | 87.36% | NA |
| Indica I | 595 | 0.50% | 0.20% | 4.20% | 95.13% | NA |
| Indica II | 465 | 1.30% | 0.00% | 3.23% | 95.48% | NA |
| Indica III | 913 | 0.90% | 3.70% | 7.23% | 88.17% | NA |
| Indica Intermediate | 786 | 1.80% | 1.10% | 4.83% | 92.24% | NA |
| Temperate Japonica | 767 | 78.20% | 0.00% | 0.00% | 21.77% | NA |
| Tropical Japonica | 504 | 11.10% | 0.00% | 0.00% | 88.89% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 1.24% | 58.92% | NA |
| VI/Aromatic | 96 | 18.80% | 2.10% | 1.04% | 78.12% | NA |
| Intermediate | 90 | 27.80% | 0.00% | 5.56% | 66.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111760 | G -> A | LOC_Os01g43830.1 | missense_variant ; p.Arg97Trp; MODERATE | nonsynonymous_codon ; R97W | Average:15.441; most accessible tissue: Minghui63 panicle, score: 38.588 | probably damaging  |
3.32 |
TOLERATED | 0.35 |
| vg0125111760 | G -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:15.441; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |