Search for Variation information by Variation ID:
Detailed information for vg0616723603:
| Variant ID: vg0616723603 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 16723603 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GCAGTGTCTAGTGCCGTCAACTCTGCTTCCATGGTTGACCTCGTCAAAATGGTCTGTTTGCAAGACCTCCACGAAACAGCACCACCACCTAGTGTGAAGG[C/A]
ATATCCACTAGTGGCTTTGATCTCATCCACATCAGAGATCCAGTTAAAATCACTATATCCTTCCAGTACCGCAGGATACCTAGAATAGTGAAGCCCCAAT
Reverse complement sequence
ATTGGGGCTTCACTATTCTAGGTATCCTGCGGTACTGGAAGGATATAGTGATTTTAACTGGATCTCTGATGTGGATGAGATCAAAGCCACTAGTGGATAT[G/T]
CCTTCACACTAGGTGGTGGTGCTGTTTCGTGGAGGTCTTGCAAACAGACCATTTTGACGAGGTCAACCATGGAAGCAGAGTTGACGGCACTAGACACTGC
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.90% | 0.60% | 0.51% | 0.02% | NA |
| All Indica | 2759 | 98.90% | 0.50% | 0.51% | 0.04% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 92.20% | 4.10% | 3.72% | 0.00% | NA |
| Indica I | 595 | 98.20% | 0.20% | 1.51% | 0.17% | NA |
| Indica II | 465 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.10% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 0.90% | 0.38% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0616723603 | C -> A | LOC_Os06g29300.1 | missense_variant ; p.Ala1122Ser; MODERATE | nonsynonymous_codon ; A1122S | Average:27.318; most accessible tissue: Zhenshan97 flower, score: 35.75 | benign  |
1.228 |
DELETERIOUS | 0.00 |
| vg0616723603 | C -> DEL | LOC_Os06g29300.1 | N | frameshift_variant | Average:27.318; most accessible tissue: Zhenshan97 flower, score: 35.75 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0616723603 | NA | 9.17E-06 | mr1062 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0616723603 | NA | 4.24E-06 | mr1215 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0616723603 | NA | 1.81E-06 | mr1510 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0616723603 | 5.97E-06 | 5.43E-06 | mr1804 | 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 |