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Detailed information for vg0505429323:

Variant ID: vg0505429323 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 5429323
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, C: 0.01, others allele: 0.00, population size: 132. )

Flanking Sequence (100 bp) in Reference Genome:


TTTGCTAGATACATCCATTTTTAAATATTACACTGTTAGACTTTATTTGGTCAAACTTTTGAAACATTGACCATCAATATCTCTCAAAATATTTTGTTTG[G/C]
GAACATAAAAATCATATTGGTAGTTTTTTTCTTTAATTGTACTTTTACAATATTAATTTTTTTAGATATTATTGTTATATTCTAATAGAAAATAGTGGTC

Reverse complement sequence

GACCACTATTTTCTATTAGAATATAACAATAATATCTAAAAAAATTAATATTGTAAAAGTACAATTAAAGAAAAAAACTACCAATATGATTTTTATGTTC[C/G]
CAAACAAAATATTTTGAGAGATATTGATGGTCAATGTTTCAAAAGTTTGACCAAATAAAGTCTAACAGTGTAATATTTAAAAATGGATGTATCTAGCAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.90% 3.60% 1.42% 0.00% NA
All Indica  2759 91.70% 6.00% 2.32% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 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 63.00% 27.50% 9.46% 0.00% NA
Indica III  913 99.50% 0.40% 0.11% 0.00% NA
Indica Intermediate  786 94.00% 4.30% 1.65% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 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 94.40% 2.20% 3.33% 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
vg0505429323 G -> C LOC_Os05g09620.1 intron_variant ; MODIFIER silent_mutation Average:42.856; most accessible tissue: Zhenshan97 young leaf, score: 65.28 N N N N
vg0505429323 G -> C LOC_Os05g09620.2 intron_variant ; MODIFIER silent_mutation Average:42.856; 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
vg0505429323 5.10E-08 NA mr1039 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
vg0505429323 2.83E-06 1.55E-11 mr1039 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
vg0505429323 NA 2.75E-06 mr1050 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
vg0505429323 NA 1.33E-10 mr1039_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
vg0505429323 NA 1.05E-07 mr1183_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
vg0505429323 NA 2.52E-07 mr1632_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