Search for Variation information by Variation ID:
Detailed information for vg0125111745:
| Variant ID: vg0125111745 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25111745 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CGACGCATTTGATGCAGCGCAGCGCACGCTTATCCGGTCCGTGACCGGTCGCAGTGTGTGACCGGTCAGATCGCGGGTTAGGTGGCAACAGGCGGCCTGT[C/T]
ACACGCCTCGCCCCGTCCCATCGAAATGATGAGAGCCTCCATGCTCTCGTCCCTAGCCGGAGCCGGCGTGTTAACTCCTGGAGTTGGCACGTCAGTCCCG
Reverse complement sequence
CGGGACTGACGTGCCAACTCCAGGAGTTAACACGCCGGCTCCGGCTAGGGACGAGAGCATGGAGGCTCTCATCATTTCGATGGGACGGGGCGAGGCGTGT[G/A]
ACAGGCCGCCTGTTGCCACCTAACCCGCGATCTGACCGGTCACACACTGCGACCGGTCACGGACCGGATAAGCGTGCGCTGCGCTGCATCAAATGCGTCG
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 | 19.10% | 1.00% | 11.17% | 68.68% | NA |
| All Indica | 2759 | 2.90% | 1.60% | 17.62% | 77.82% | NA |
| All Japonica | 1512 | 49.70% | 0.00% | 0.33% | 49.93% | NA |
| Aus | 269 | 10.00% | 0.00% | 9.67% | 80.30% | NA |
| Indica I | 595 | 1.80% | 0.20% | 8.74% | 89.24% | NA |
| Indica II | 465 | 3.40% | 0.20% | 23.23% | 73.12% | NA |
| Indica III | 913 | 3.00% | 3.70% | 19.61% | 73.71% | NA |
| Indica Intermediate | 786 | 3.40% | 1.10% | 18.70% | 76.72% | NA |
| Temperate Japonica | 767 | 78.20% | 0.00% | 0.00% | 21.77% | NA |
| Tropical Japonica | 504 | 10.90% | 0.00% | 0.79% | 88.29% | NA |
| Japonica Intermediate | 241 | 40.20% | 0.00% | 0.41% | 59.34% | NA |
| VI/Aromatic | 96 | 18.80% | 2.10% | 0.00% | 79.17% | NA |
| Intermediate | 90 | 30.00% | 0.00% | 12.22% | 57.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111745 | C -> T | LOC_Os01g43830.1 | missense_variant ; p.Asp102Asn; MODERATE | nonsynonymous_codon ; D102N | Average:16.003; most accessible tissue: Minghui63 panicle, score: 38.588 | possibly damaging  |
1.641 |
TOLERATED | 0.57 |
| vg0125111745 | C -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:16.003; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |