Search for Variation information by Variation ID:
Detailed information for vg0513378621:
| Variant ID: vg0513378621 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 13378621 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 131. )
Flanking Sequence (100 bp) in Reference Genome:
GTCATGGCTATTACTTACCAGGCCAAGAGCTTCTGCAGCAGTTCTGATATTACCAGCAGTACAGATGCTCCTATATAGAGATAAGAGATGAACCCTTTCC[G/A]
CAACTTGTAAATTCTTCTTAAGTCCACCAGCAACCATTTCCATTTCCGCCTGTAGGGGACAAAGAAACAAAAAGTTGCATAAATATGTTTCCATTAAGAG
Reverse complement sequence
CTCTTAATGGAAACATATTTATGCAACTTTTTGTTTCTTTGTCCCCTACAGGCGGAAATGGAAATGGTTGCTGGTGGACTTAAGAAGAATTTACAAGTTG[C/T]
GGAAAGGGTTCATCTCTTATCTCTATATAGGAGCATCTGTACTGCTGGTAATATCAGAACTGCTGCAGAAGCTCTTGGCCTGGTAAGTAATAGCCATGAC
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 | 94.60% | 4.90% | 0.44% | 0.00% | NA |
| All Indica | 2759 | 90.80% | 8.40% | 0.72% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 82.50% | 15.50% | 2.02% | 0.00% | NA |
| Indica II | 465 | 94.40% | 4.90% | 0.65% | 0.00% | NA |
| Indica III | 913 | 93.50% | 6.40% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 91.90% | 7.60% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.13% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0513378621 | G -> A | LOC_Os05g23420.1 | missense_variant ; p.Ala412Val; MODERATE | nonsynonymous_codon ; A412V | Average:63.033; most accessible tissue: Minghui63 flag leaf, score: 74.955 | possibly damaging  |
1.521 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0513378621 | NA | 9.23E-07 | mr1125 | 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 |
| vg0513378621 | 3.07E-06 | 3.08E-06 | mr1160 | 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 |
| vg0513378621 | 1.32E-06 | 6.57E-09 | mr1593 | 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 |
| vg0513378621 | 2.63E-06 | 1.28E-08 | mr1593 | 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 |
| vg0513378621 | 2.85E-06 | NA | mr1593_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 |
| vg0513378621 | 5.15E-06 | 5.96E-08 | mr1593_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 |