Search for Variation information by Variation ID:
Detailed information for vg0125111981:
| Variant ID: vg0125111981 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25111981 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AAGGAAGTCATTGTATGAAGAAGGGCAGACGTGCGGCGTGCTAAACTGACACGTGGTGGACAAGAATGACCGGTCTGTGACTGGTCTGACGCCGGTCACG[T/A]
CATCGGCAGACAACCGAGCTCCCACGTTGCATCTGCTTCCGGCGGAGTGGAGGTAGATATGACCCATCCCATCGGAGGGTCATTCGGACAGCAGCCATTG
Reverse complement sequence
CAATGGCTGCTGTCCGAATGACCCTCCGATGGGATGGGTCATATCTACCTCCACTCCGCCGGAAGCAGATGCAACGTGGGAGCTCGGTTGTCTGCCGATG[A/T]
CGTGACCGGCGTCAGACCAGTCACAGACCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCACGCCGCACGTCTGCCCTTCTTCATACAATGACTTCCTT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.00% | 0.30% | 5.92% | 46.78% | NA |
| All Indica | 2759 | 34.60% | 0.20% | 8.63% | 56.58% | NA |
| All Japonica | 1512 | 74.30% | 0.10% | 0.73% | 24.93% | NA |
| Aus | 269 | 3.70% | 1.90% | 9.29% | 85.13% | NA |
| Indica I | 595 | 30.60% | 0.00% | 5.55% | 63.87% | NA |
| Indica II | 465 | 55.30% | 0.00% | 7.74% | 36.99% | NA |
| Indica III | 913 | 23.90% | 0.20% | 12.16% | 63.75% | NA |
| Indica Intermediate | 786 | 37.80% | 0.50% | 7.38% | 54.33% | NA |
| Temperate Japonica | 767 | 98.20% | 0.00% | 0.00% | 1.83% | NA |
| Tropical Japonica | 504 | 43.50% | 0.00% | 1.59% | 54.96% | NA |
| Japonica Intermediate | 241 | 62.70% | 0.40% | 1.24% | 35.68% | NA |
| VI/Aromatic | 96 | 86.50% | 0.00% | 0.00% | 13.54% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 6.67% | 34.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111981 | T -> A | LOC_Os01g43830.1 | missense_variant ; p.Asp23Val; MODERATE | nonsynonymous_codon ; D23V | Average:6.906; most accessible tissue: Zhenshan97 panicle, score: 16.188 | probably damaging  |
2.171 |
DELETERIOUS | 0.00 |
| vg0125111981 | T -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:6.906; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |