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Detailed information for vg0417136797:

Variant ID: vg0417136797 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 17136797
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGCTGAAGGTTCTACTACTATGACATCCAGCTTCATCGACAACAGCGTCAACACCAACCTCAACCAGGGAGTTCCTGCTTCAACAATGCTGGTGTGGA[C/T]
TCAAGTCGGCGAAATCGTCTTCCCGGTTTACACCATGATGCCGATCTCAGCCGGTCCATCAATGGCCGGAAACAAGAACGCAGTGGCTACAGCCTAGGAT

Reverse complement sequence

ATCCTAGGCTGTAGCCACTGCGTTCTTGTTTCCGGCCATTGATGGACCGGCTGAGATCGGCATCATGGTGTAAACCGGGAAGACGATTTCGCCGACTTGA[G/A]
TCCACACCAGCATTGTTGAAGCAGGAACTCCCTGGTTGAGGTTGGTGTTGACGCTGTTGTCGATGAAGCTGGATGTCATAGTAGTAGAACCTTCAGCACC

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 97.70% 1.80% 0.55% 0.00% NA
All Indica  2759 96.00% 3.00% 0.94% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.70% 11.60% 3.70% 0.00% NA
Indica II  465 99.60% 0.00% 0.43% 0.00% NA
Indica III  913 99.70% 0.20% 0.11% 0.00% NA
Indica Intermediate  786 98.30% 1.50% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 97.80% 2.20% 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
vg0417136797 C -> T LOC_Os04g28910.1 upstream_gene_variant ; 107.0bp to feature; MODIFIER silent_mutation Average:50.39; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N
vg0417136797 C -> T LOC_Os04g28900-LOC_Os04g28910 intergenic_region ; MODIFIER silent_mutation Average:50.39; most accessible tissue: Zhenshan97 young leaf, score: 67.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0417136797 NA 9.02E-06 mr1335 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
vg0417136797 3.06E-06 NA mr1532 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
vg0417136797 NA 3.78E-06 mr1904 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
vg0417136797 NA 8.48E-06 mr1502_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