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Detailed information for vg0607815296:

Variant ID: vg0607815296 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 7815296
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.67, A: 0.33, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAAAAATGAATTTGTTTTTATTTTTTAAGGTAACTCCTATATAAAATGTTTTTTTTCATAAATACATCGTTTAGTAGTTTAAAAAAAATATGCTAACA[A/G]
AAAATAAGAAAGTAGGCAAACCGAACGCAGTTTAGAACGGACCATAAGATGAATAAGTTCAATATATGAGTTGGGTGAATACATTGGATAAACTCCAAAT

Reverse complement sequence

ATTTGGAGTTTATCCAATGTATTCACCCAACTCATATATTGAACTTATTCATCTTATGGTCCGTTCTAAACTGCGTTCGGTTTGCCTACTTTCTTATTTT[T/C]
TGTTAGCATATTTTTTTTAAACTACTAAACGATGTATTTATGAAAAAAAACATTTTATATAGGAGTTACCTTAAAAAATAAAAACAAATTCATTTTTTCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.20% 42.50% 0.06% 0.30% NA
All Indica  2759 32.10% 67.40% 0.07% 0.43% NA
All Japonica  1512 99.10% 0.80% 0.00% 0.07% NA
Aus  269 84.80% 15.20% 0.00% 0.00% NA
Indica I  595 13.30% 85.70% 0.17% 0.84% NA
Indica II  465 72.50% 27.10% 0.00% 0.43% NA
Indica III  913 19.30% 80.10% 0.11% 0.55% NA
Indica Intermediate  786 37.40% 62.60% 0.00% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.50% 2.10% 0.00% 0.41% NA
VI/Aromatic  96 20.80% 79.20% 0.00% 0.00% NA
Intermediate  90 76.70% 21.10% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0607815296 A -> G LOC_Os06g14030-LOC_Os06g14040 intergenic_region ; MODIFIER silent_mutation Average:54.295; most accessible tissue: Callus, score: 75.345 N N N N
vg0607815296 A -> DEL N N silent_mutation Average:54.295; most accessible tissue: Callus, score: 75.345 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0607815296 NA 7.59E-15 mr1133_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
vg0607815296 NA 6.82E-07 mr1185_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
vg0607815296 NA 7.34E-08 mr1269_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
vg0607815296 NA 8.25E-07 mr1272_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
vg0607815296 NA 1.81E-06 mr1355_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
vg0607815296 NA 3.79E-08 mr1399_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
vg0607815296 NA 1.18E-07 mr1457_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
vg0607815296 NA 2.27E-07 mr1458_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
vg0607815296 NA 9.69E-09 mr1478_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
vg0607815296 NA 1.24E-07 mr1479_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
vg0607815296 NA 2.36E-07 mr1662_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
vg0607815296 NA 3.19E-08 mr1677_2 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
vg0607815296 NA 2.55E-14 mr1726_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
vg0607815296 NA 3.79E-09 mr1860_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
vg0607815296 NA 4.91E-14 mr1950_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