Search for Variation information by Variation ID:
Detailed information for vg0404609763:
| Variant ID: vg0404609763 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 4609763 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTGGTGGTGTGATTGAACTGGGAATTATTTCAGAAGGTTGGCTAGAACTACTATGTGTATTCTTCATTGGGAAAAAGCTCTCAAAGAAGTTAGCATCAC[G/A]
AGACTCCATAATTGTACCAACATGCATGTCAGTTACCTCAGATTTAACTATTAAAAATCTATAGGCAATGATGTGATGAGCATATCCCAGAAAGACACAG
Reverse complement sequence
CTGTGTCTTTCTGGGATATGCTCATCACATCATTGCCTATAGATTTTTAATAGTTAAATCTGAGGTAACTGACATGCATGTTGGTACAATTATGGAGTCT[C/T]
GTGATGCTAACTTCTTTGAGAGCTTTTTCCCAATGAAGAATACACATAGTAGTTCTAGCCAACCTTCTGAAATAATTCCCAGTTCAATCACACCACCAGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.60% | 0.20% | 5.73% | 7.51% | NA |
| All Indica | 2759 | 79.90% | 0.30% | 8.59% | 11.24% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.46% | 1.98% | NA |
| Aus | 269 | 86.20% | 0.00% | 8.92% | 4.83% | NA |
| Indica I | 595 | 94.80% | 0.00% | 2.69% | 2.52% | NA |
| Indica II | 465 | 84.90% | 0.20% | 4.73% | 10.11% | NA |
| Indica III | 913 | 67.60% | 0.30% | 14.46% | 17.63% | NA |
| Indica Intermediate | 786 | 79.90% | 0.50% | 8.52% | 11.07% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 1.39% | 5.56% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 0.00% | 3.33% | 2.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0404609763 | G -> DEL | LOC_Os04g08520.1 | N | frameshift_variant | Average:22.939; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | N | N | N | N |
| vg0404609763 | G -> A | LOC_Os04g08520.1 | missense_variant ; p.Arg263Cys; MODERATE | nonsynonymous_codon ; R263C | Average:22.939; most accessible tissue: Zhenshan97 flag leaf, score: 31.305 | probably damaging  |
2.912 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0404609763 | NA | 1.41E-07 | mr1798 | 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 |
| vg0404609763 | 6.09E-07 | NA | mr1037_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 |
| vg0404609763 | 2.61E-07 | 2.33E-08 | mr1037_2 | 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 |
| vg0404609763 | 1.38E-07 | NA | mr1798_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 |
| vg0404609763 | 2.12E-08 | 1.20E-14 | mr1798_2 | 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 |