Search for Variation information by Variation ID:
Detailed information for vg0125111853:
| Variant ID: vg0125111853 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25111853 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 109. )
Flanking Sequence (100 bp) in Reference Genome:
TCGCCCCGTCCCATCGAAATGATGAGAGCCTCCATGCTCTCGTCCCTAGCCGGAGCCGGCGTGTTAACTCCTGGAGTTGGCACGTCAGTCCCGGCCAGAT[A/T]
CATTCCAGGCTTCATCGCAACCATTGCAAGGAAGTCATTGTATGAAGAAGGGCAGACGTGCGGCGTGCTAAACTGACACGTGGTGGACAAGAATGACCGG
Reverse complement sequence
CCGGTCATTCTTGTCCACCACGTGTCAGTTTAGCACGCCGCACGTCTGCCCTTCTTCATACAATGACTTCCTTGCAATGGTTGCGATGAAGCCTGGAATG[T/A]
ATCTGGCCGGGACTGACGTGCCAACTCCAGGAGTTAACACGCCGGCTCCGGCTAGGGACGAGAGCATGGAGGCTCTCATCATTTCGATGGGACGGGGCGA
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 | 0.50% | 0.40% | 2.81% | 96.28% | NA |
| All Indica | 2759 | 0.90% | 0.30% | 4.28% | 94.53% | NA |
| All Japonica | 1512 | 0.00% | 0.60% | 0.86% | 98.54% | NA |
| Aus | 269 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica I | 595 | 0.50% | 0.20% | 0.84% | 98.49% | NA |
| Indica II | 465 | 1.90% | 0.20% | 6.45% | 91.40% | NA |
| Indica III | 913 | 0.90% | 0.30% | 5.37% | 93.43% | NA |
| Indica Intermediate | 786 | 0.60% | 0.40% | 4.33% | 94.66% | NA |
| Temperate Japonica | 767 | 0.00% | 1.00% | 1.56% | 97.39% | NA |
| Tropical Japonica | 504 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.40% | 0.41% | 99.17% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 0.00% | 1.10% | 2.22% | 96.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111853 | A -> T | LOC_Os01g43830.1 | missense_variant ; p.Tyr66Asn; MODERATE | nonsynonymous_codon ; Y66N | Average:15.027; most accessible tissue: Minghui63 panicle, score: 38.588 | benign  |
-0.096 |
TOLERATED | 1.00 |
| vg0125111853 | A -> DEL | LOC_Os01g43830.1 | N | frameshift_variant | Average:15.027; most accessible tissue: Minghui63 panicle, score: 38.588 | N | N | N | N |