Search for Variation information by Variation ID:
Detailed information for vg0324081878:
| Variant ID: vg0324081878 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 24081878 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ACTGGAAGGTGCTACAGTTTTCTCCAAGATAGATCTTCGTTCTGGATATCACCAACTCCGAATCCGTGAGGAGGATATACCAAAGACCGCCTTTACAACA[C/T]
GGTATGGTTTGTTTGAGTGTACCGTTATGTCGTTCGGACTCACTAATGCCCCGGCCTTTTTCATGAACCTGATGAACAAAATGTTTATGGAATATCTGGA
Reverse complement sequence
TCCAGATATTCCATAAACATTTTGTTCATCAGGTTCATGAAAAAGGCCGGGGCATTAGTGAGTCCGAACGACATAACGGTACACTCAAACAAACCATACC[G/A]
TGTTGTAAAGGCGGTCTTTGGTATATCCTCCTCACGGATTCGGAGTTGGTGATATCCAGAACGAAGATCTATCTTGGAGAAAACTGTAGCACCTTCCAGT
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 | 53.80% | 3.70% | 40.12% | 2.31% | NA |
| All Indica | 2759 | 26.60% | 2.80% | 66.73% | 3.84% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.53% | 0.00% | NA |
| Aus | 269 | 56.50% | 36.10% | 7.43% | 0.00% | NA |
| Indica I | 595 | 30.90% | 1.30% | 65.88% | 1.85% | NA |
| Indica II | 465 | 22.60% | 4.30% | 64.09% | 9.03% | NA |
| Indica III | 913 | 22.70% | 2.70% | 70.87% | 3.72% | NA |
| Indica Intermediate | 786 | 30.40% | 3.10% | 64.12% | 2.42% | NA |
| Temperate Japonica | 767 | 99.60% | 0.00% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 66.70% | 3.30% | 26.67% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324081878 | C -> T | LOC_Os03g43160.1 | missense_variant ; p.Arg522Trp; MODERATE | nonsynonymous_codon ; R522W | Average:17.553; most accessible tissue: Zhenshan97 root, score: 22.162 | benign  |
1.292 |
DELETERIOUS | 0.01 |
| vg0324081878 | C -> DEL | LOC_Os03g43160.1 | N | frameshift_variant | Average:17.553; most accessible tissue: Zhenshan97 root, score: 22.162 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0324081878 | NA | 3.08E-06 | mr1050 | 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 |
| vg0324081878 | 8.76E-06 | 1.39E-06 | mr1272 | 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 |