Search for Variation information by Variation ID:
Detailed information for vg0300021861:
| Variant ID: vg0300021861 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21861 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 327. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTGGGACTAGCAGATGATCTCGCAGCCAAGACGTGACCACCCAAGGCTCACATTCAGAGTTGCCAATCTTTGCATCTATGGCATTATCTTCAAGGACC[T/C]
CACACACCTATTGTATGAGAACAGGCAAAAGACAAATACAAGAAGGTCCAAAGAAGTTATGGAAAAATTAAAATGCAACAAACAAATGATTTACTACTGT
Reverse complement sequence
ACAGTAGTAAATCATTTGTTTGTTGCATTTTAATTTTTCCATAACTTCTTTGGACCTTCTTGTATTTGTCTTTTGCCTGTTCTCATACAATAGGTGTGTG[A/G]
GGTCCTTGAAGATAATGCCATAGATGCAAAGATTGGCAACTCTGAATGTGAGCCTTGGGTGGTCACGTCTTGGCTGCGAGATCATCTGCTAGTCCCACAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.00% | 0.90% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 97.00% | 2.60% | 0.33% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.10% | 7.10% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.20% | 0.41% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0300021861 | T -> C | LOC_Os03g01016.2 | missense_variant ; p.Glu253Gly; MODERATE | nonsynonymous_codon ; E253G | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.636 |
TOLERATED | 0.06 |
| vg0300021861 | T -> C | LOC_Os03g01016.1 | missense_variant ; p.Arg251Gly; MODERATE | nonsynonymous_codon ; R251G | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.03 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0300021861 | NA | 1.92E-06 | mr1543 | 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 |
| vg0300021861 | 3.02E-06 | 5.15E-07 | mr1871 | Jap_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 |
| vg0300021861 | NA | 9.75E-07 | mr1951 | 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 |
| vg0300021861 | 2.48E-06 | NA | mr1871_2 | Jap_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 |