Search for Variation information by Variation ID:
Detailed information for vg0141809199:
| Variant ID: vg0141809199 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 41809199 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TAGTCGCCGTACACCATGGCCCCTGTGAGCCCCAGGGATCGCAGGCCCGCCAGGCGGTCGAGGACGGCGTCATAGCCATCTCCCAGATCTACCGGCGCCC[G/A]
CCAGCTGGAGGCCTGCCCCGGGGGCTGGCTCGGAAGTCGGAGGCGCGCTTCGTCGGCGAGGGGGGTGTAGAACCAGTCGCTCTTCCAGTCATCCCACTTC
Reverse complement sequence
GAAGTGGGATGACTGGAAGAGCGACTGGTTCTACACCCCCCTCGCCGACGAAGCGCGCCTCCGACTTCCGAGCCAGCCCCCGGGGCAGGCCTCCAGCTGG[C/T]
GGGCGCCGGTAGATCTGGGAGATGGCTATGACGCCGTCCTCGACCGCCTGGCGGGCCTGCGATCCCTGGGGCTCACAGGGGCCATGGTGTACGGCGACTA
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 | 27.50% | 0.10% | 4.02% | 68.32% | NA |
| All Indica | 2759 | 17.40% | 0.30% | 5.65% | 76.66% | NA |
| All Japonica | 1512 | 44.40% | 0.00% | 0.99% | 54.56% | NA |
| Aus | 269 | 37.50% | 0.00% | 5.20% | 57.25% | NA |
| Indica I | 595 | 11.80% | 0.20% | 6.72% | 81.34% | NA |
| Indica II | 465 | 12.50% | 0.00% | 3.01% | 84.52% | NA |
| Indica III | 913 | 25.00% | 0.50% | 6.79% | 67.69% | NA |
| Indica Intermediate | 786 | 15.90% | 0.10% | 5.09% | 78.88% | NA |
| Temperate Japonica | 767 | 77.20% | 0.00% | 0.39% | 22.43% | NA |
| Tropical Japonica | 504 | 5.40% | 0.00% | 1.79% | 92.86% | NA |
| Japonica Intermediate | 241 | 22.00% | 0.00% | 1.24% | 76.76% | NA |
| VI/Aromatic | 96 | 17.70% | 0.00% | 0.00% | 82.29% | NA |
| Intermediate | 90 | 32.20% | 0.00% | 5.56% | 62.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0141809199 | G -> A | LOC_Os01g72070.1 | missense_variant ; p.Arg125Trp; MODERATE | nonsynonymous_codon ; R125W | Average:5.279; most accessible tissue: Callus, score: 13.399 | probably damaging  |
2.965 |
DELETERIOUS | 0.01 |
| vg0141809199 | G -> DEL | LOC_Os01g72070.1 | N | frameshift_variant | Average:5.279; most accessible tissue: Callus, score: 13.399 | N | N | N | N |