Search for Variation information by Variation ID:
Detailed information for vg0332720125:
| Variant ID: vg0332720125 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 32720125 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TATCCCTCAATCCTGATGAAACTTCCTGATGATTTGGCCGCTGTTTTCACTGTCAAGACATCTCCCACTCGAAGATCTAGGAGAGCTCCGGCTTCGGCCC[C/T]
GATCCAATCTAGATCCAGAGAGGTTGGCGTTATACTCCAACCTCTTGGGACAGTCTCGACGGAAGAGTTGGATGGTTACCTTAGCTCCCCCGGCGTCAGT
Reverse complement sequence
ACTGACGCCGGGGGAGCTAAGGTAACCATCCAACTCTTCCGTCGAGACTGTCCCAAGAGGTTGGAGTATAACGCCAACCTCTCTGGATCTAGATTGGATC[G/A]
GGGCCGAAGCCGGAGCTCTCCTAGATCTTCGAGTGGGAGATGTCTTGACAGTGAAAACAGCGGCCAAATCATCAGGAAGTTTCATCAGGATTGAGGGATA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.40% | 5.20% | 0.36% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 0.80% | 0.33% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 16.00% | 81.00% | 2.97% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.10% | 0.40% | 1.51% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.20% | 1.50% | 0.25% | 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 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0332720125 | C -> T | LOC_Os03g57370.1 | missense_variant ; p.Pro124Leu; MODERATE | nonsynonymous_codon ; P124L | Average:23.118; most accessible tissue: Minghui63 root, score: 36.81 | benign  |
0.56 |
DELETERIOUS | 0.02 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0332720125 | NA | 6.07E-06 | mr1230 | 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 |
| vg0332720125 | 3.88E-06 | NA | mr1496 | 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 |
| vg0332720125 | NA | 1.67E-06 | mr1556 | 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 |
| vg0332720125 | 2.07E-06 | NA | mr1526_2 | 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 |
| vg0332720125 | NA | 6.75E-10 | mr1649_2 | 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 |