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Detailed information for vg0607527077:

Variant ID: vg0607527077 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 7527077
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, G: 0.38, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


AATTAGTATGAGTGATAGTTTATTCAACATGCCTTCCTCTCAATCACTAGTCTAGCTAGCTAATCTGTCATCTACTGTACTTTCTAAATTGCTAGCTATA[G/T]
CTATTTATATAGATTTTAGAGTCATGTGCGCTGTGTCATATATATATTTCTTATTTTGTTAGCTAAAAGTTGGTATGGGTTCAAATATGAGAAAATCTAT

Reverse complement sequence

ATAGATTTTCTCATATTTGAACCCATACCAACTTTTAGCTAACAAAATAAGAAATATATATATGACACAGCGCACATGACTCTAAAATCTATATAAATAG[C/A]
TATAGCTAGCAATTTAGAAAGTACAGTAGATGACAGATTAGCTAGCTAGACTAGTGATTGAGAGGAAGGCATGTTGAATAAACTATCACTCATACTAATT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 60.80% 39.20% 0.02% 0.00% NA
All Indica  2759 36.80% 63.20% 0.04% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 33.60% 66.20% 0.17% 0.00% NA
Indica II  465 66.20% 33.80% 0.00% 0.00% NA
Indica III  913 18.10% 81.90% 0.00% 0.00% NA
Indica Intermediate  786 43.40% 56.60% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.50% 0.00% 0.00% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0607527077 G -> T LOC_Os06g13600.1 upstream_gene_variant ; 3757.0bp to feature; MODIFIER silent_mutation Average:36.209; most accessible tissue: Callus, score: 86.201 N N N N
vg0607527077 G -> T LOC_Os06g13590-LOC_Os06g13600 intergenic_region ; MODIFIER silent_mutation Average:36.209; most accessible tissue: Callus, score: 86.201 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0607527077 NA 2.82E-06 mr1874_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
vg0607527077 7.05E-08 NA mr1970_2 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
vg0607527077 4.08E-07 1.33E-08 mr1970_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
vg0607527077 9.46E-09 NA mr1973_2 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
vg0607527077 1.96E-07 2.07E-08 mr1973_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