Search for Variation information by Variation ID:
Detailed information for vg0329922975:
| Variant ID: vg0329922975 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 29922975 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )
Flanking Sequence (100 bp) in Reference Genome:
GGCAAAGAGGAAAACCAAGTAAAAGCTGATCCAGACAGAGATAACCGGAATAACCTAAATCTCAGAGCGTCTACAGCCGATGCTTCACCACACTGAGCAA[G/T]
GAATCGGTTGATGTGCTCATAAGTTGACACGCCCTCTTGTCCCGAAAACTTGGAGAAATCTGGAACTTTAAACCGATTGGGGAGAGGAACTCTTTCAAAC
Reverse complement sequence
GTTTGAAAGAGTTCCTCTCCCCAATCGGTTTAAAGTTCCAGATTTCTCCAAGTTTTCGGGACAAGAGGGCGTGTCAACTTATGAGCACATCAACCGATTC[C/A]
TTGCTCAGTGTGGTGAAGCATCGGCTGTAGACGCTCTGAGATTTAGGTTATTCCGGTTATCTCTGTCTGGATCAGCTTTTACTTGGTTTTCCTCTTTGCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 86.50% | 1.00% | 12.51% | 0.02% | NA |
| All Indica | 2759 | 77.30% | 1.70% | 20.91% | 0.04% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 71.30% | 1.00% | 27.73% | 0.00% | NA |
| Indica II | 465 | 68.40% | 2.40% | 29.03% | 0.22% | NA |
| Indica III | 913 | 83.00% | 1.80% | 15.22% | 0.00% | NA |
| Indica Intermediate | 786 | 80.70% | 1.80% | 17.56% | 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 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 1.10% | 11.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0329922975 | G -> T | LOC_Os03g52110.1 | missense_variant ; p.Leu266Ile; MODERATE | nonsynonymous_codon ; L266I | Average:31.374; most accessible tissue: Minghui63 root, score: 49.234 | benign  |
1.032 |
DELETERIOUS | 0.04 |
| vg0329922975 | G -> DEL | LOC_Os03g52110.1 | N | frameshift_variant | Average:31.374; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0329922975 | 7.48E-07 | 5.40E-08 | mr1771 | 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 |