Search for Variation information by Variation ID:
Detailed information for vg0216380020:
| Variant ID: vg0216380020 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 16380020 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCAGTAGGCCCCAAAGGGCGTGATGAATGAAGTCTTCAAGCAGTCGGATTCCTTCAGTCGGATCTGATGATATCCCGAGTAGCAATCCAAAAAACTGAGT[A/C]
GCTCGCAGCCGGCGGTCGAGTCGACCACCTGGTCAATGCGAGGGAACCCGAAGGGATCTTTGGGACAAGACTTGTTGAGGTTGGTGTAATCGACACACAT
Reverse complement sequence
ATGTGTGTCGATTACACCAACCTCAACAAGTCTTGTCCCAAAGATCCCTTCGGGTTCCCTCGCATTGACCAGGTGGTCGACTCGACCGCCGGCTGCGAGC[T/G]
ACTCAGTTTTTTGGATTGCTACTCGGGATATCATCAGATCCGACTGAAGGAATCCGACTGCTTGAAGACTTCATTCATCACGCCCTTTGGGGCCTACTGC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 0.40% | 1.33% | 0.55% | NA |
| All Indica | 2759 | 96.10% | 0.70% | 2.28% | 0.94% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 95.80% | 0.50% | 2.18% | 1.51% | NA |
| Indica II | 465 | 92.90% | 0.90% | 4.30% | 1.94% | NA |
| Indica III | 913 | 98.00% | 0.50% | 0.99% | 0.44% | NA |
| Indica Intermediate | 786 | 96.10% | 0.80% | 2.67% | 0.51% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0216380020 | A -> DEL | LOC_Os02g27640.1 | N | frameshift_variant | Average:44.607; most accessible tissue: Minghui63 young leaf, score: 69.4 | N | N | N | N |
| vg0216380020 | A -> C | LOC_Os02g27640.1 | missense_variant ; p.Leu34Arg; MODERATE | nonsynonymous_codon ; L34R | Average:44.607; most accessible tissue: Minghui63 young leaf, score: 69.4 | probably damaging  |
2.216 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0216380020 | 8.09E-07 | NA | mr1321 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0216380020 | 3.06E-06 | 3.06E-06 | mr1321 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0216380020 | 1.92E-06 | NA | mr1972 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0216380020 | 4.41E-06 | 4.41E-06 | mr1972 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |