Search for Variation information by Variation ID:
Detailed information for vg0331795700:
| Variant ID: vg0331795700 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 31795700 |
| 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: 300. )
Flanking Sequence (100 bp) in Reference Genome:
AACAACAACAAGTCGAAGGGTTCATACAAAGGGAGGAAGATGGAGAATCTTAGGAAGGCTTTTCAACAAGTTTGCGCCGCCTTCGAGCCACTAAGTGATG[T/C]
AGATGGTGAAAGAGGAGATGATGATAAGGGAAACAACATCTCCGATGTTTGCTTCATGGCGCGTGGTGAATCTGACACAGAGTATGAAGATAATGAGGTG
Reverse complement sequence
CACCTCATTATCTTCATACTCTGTGTCAGATTCACCACGCGCCATGAAGCAAACATCGGAGATGTTGTTTCCCTTATCATCATCTCCTCTTTCACCATCT[A/G]
CATCACTTAGTGGCTCGAAGGCGGCGCAAACTTGTTGAAAAGCCTTCCTAAGATTCTCCATCTTCCTCCCTTTGTATGAACCCTTCGACTTGTTGTTGTT
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 | 96.60% | 2.20% | 1.21% | 0.00% | NA |
| All Indica | 2759 | 94.60% | 3.50% | 1.92% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.00% | 0.00% | 1.01% | 0.00% | NA |
| Indica II | 465 | 84.10% | 11.40% | 4.52% | 0.00% | NA |
| Indica III | 913 | 96.30% | 3.00% | 0.77% | 0.00% | NA |
| Indica Intermediate | 786 | 95.40% | 2.20% | 2.42% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.40% | 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 | 93.30% | 4.40% | 2.22% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0331795700 | T -> C | LOC_Os03g55860.1 | missense_variant ; p.Val245Ala; MODERATE | nonsynonymous_codon ; V245A | Average:15.993; most accessible tissue: Minghui63 panicle, score: 29.741 | benign  |
1.284 |
TOLERATED | 0.06 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0331795700 | NA | 2.03E-08 | mr1829 | 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 |
| vg0331795700 | 1.88E-06 | 5.47E-13 | mr1829_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 |
| vg0331795700 | NA | 4.53E-07 | mr1842_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 |
| vg0331795700 | 3.89E-07 | 4.55E-13 | mr1902_2 | 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 |