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Detailed information for vg0317860149:

Variant ID: vg0317860149 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 17860149
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


AAACTATTTTGATTTCTTTAGGGAATATCTCCTAGTTACCATTAAAATGGTCATGAAAAATTCTCAAAAATTTGATCACAAGATATCTCTGGAAGTAAAA[C/T]
ATTTCTATACTAGATGGTACCCTGTGCGTTGCTGCAAAAATTGGTAAGAAATATTCAACATGAAAAATATTATAGGTGATATATCTTAGGAGAAGTAGGA

Reverse complement sequence

TCCTACTTCTCCTAAGATATATCACCTATAATATTTTTCATGTTGAATATTTCTTACCAATTTTTGCAGCAACGCACAGGGTACCATCTAGTATAGAAAT[G/A]
TTTTACTTCCAGAGATATCTTGTGATCAAATTTTTGAGAATTTTTCATGACCATTTTAATGGTAACTAGGAGATATTCCCTAAAGAAATCAAAATAGTTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 4.10% 0.00% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 87.60% 12.40% 0.00% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 65.90% 34.10% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0317860149 C -> T LOC_Os03g31340.1 upstream_gene_variant ; 668.0bp to feature; MODIFIER silent_mutation Average:46.677; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N
vg0317860149 C -> T LOC_Os03g31360.1 upstream_gene_variant ; 4129.0bp to feature; MODIFIER silent_mutation Average:46.677; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N
vg0317860149 C -> T LOC_Os03g31340-LOC_Os03g31360 intergenic_region ; MODIFIER silent_mutation Average:46.677; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0317860149 NA 4.56E-06 mr1073 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
vg0317860149 NA 3.55E-06 mr1227 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
vg0317860149 1.23E-07 1.23E-07 mr1362 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
vg0317860149 NA 1.19E-06 mr1583 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
vg0317860149 NA 1.89E-07 mr1696 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
vg0317860149 NA 7.54E-07 mr1830 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
vg0317860149 2.84E-06 2.97E-11 mr1852 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