Search for Variation information by Variation ID:
Detailed information for vg0403323241:
| Variant ID: vg0403323241 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 3323241 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 58. )
Flanking Sequence (100 bp) in Reference Genome:
AGGTGCCACCGTTTTCTCCAAGATAGATCTTCGATCAGGGTATCACCAGTTAAGGATCAAAGAGGAAGATATACCTAAGACAGCTTTTACCACTAGGTAT[A/G]
GGTTGTTTGAATGTACTGTTATGTCTTTTGGACTTACCAATGCCCCCGCTTTCTTCATGAACTTGATGAATAAGGTGTTTATGGAATACCTGGATAAGTT
Reverse complement sequence
AACTTATCCAGGTATTCCATAAACACCTTATTCATCAAGTTCATGAAGAAAGCGGGGGCATTGGTAAGTCCAAAAGACATAACAGTACATTCAAACAACC[T/C]
ATACCTAGTGGTAAAAGCTGTCTTAGGTATATCTTCCTCTTTGATCCTTAACTGGTGATACCCTGATCGAAGATCTATCTTGGAGAAAACGGTGGCACCT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 18.60% | 16.80% | 14.28% | 50.34% | NA |
| All Indica | 2759 | 7.80% | 17.60% | 19.93% | 54.69% | NA |
| All Japonica | 1512 | 42.10% | 16.80% | 1.46% | 39.68% | NA |
| Aus | 269 | 4.10% | 12.30% | 22.68% | 60.97% | NA |
| Indica I | 595 | 10.30% | 3.70% | 16.13% | 69.92% | NA |
| Indica II | 465 | 6.70% | 27.70% | 12.69% | 52.90% | NA |
| Indica III | 913 | 8.80% | 18.70% | 24.97% | 47.54% | NA |
| Indica Intermediate | 786 | 5.30% | 20.90% | 21.25% | 52.54% | NA |
| Temperate Japonica | 767 | 75.50% | 12.40% | 1.04% | 11.08% | NA |
| Tropical Japonica | 504 | 3.80% | 17.90% | 1.79% | 76.59% | NA |
| Japonica Intermediate | 241 | 15.80% | 28.60% | 2.07% | 53.53% | NA |
| VI/Aromatic | 96 | 5.20% | 4.20% | 30.21% | 60.42% | NA |
| Intermediate | 90 | 13.30% | 18.90% | 14.44% | 53.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0403323241 | A -> DEL | LOC_Os04g06360.1 | N | frameshift_variant | Average:24.349; most accessible tissue: Minghui63 flag leaf, score: 55.781 | N | N | N | N |
| vg0403323241 | A -> G | LOC_Os04g06360.1 | missense_variant ; p.Arg1110Gly; MODERATE | nonsynonymous_codon ; R1110G | Average:24.349; most accessible tissue: Minghui63 flag leaf, score: 55.781 | benign  |
-1.021 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0403323241 | NA | 1.52E-09 | Heading_date | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0403323241 | NA | 3.85E-11 | Plant_height | Jap_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0403323241 | 4.73E-08 | 2.38E-07 | mr1865 | 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 |
| vg0403323241 | NA | 1.51E-07 | mr1010_2 | Jap_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 |
| vg0403323241 | NA | 3.21E-07 | mr1521_2 | Jap_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 |