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Detailed information for vg0506861028:

Variant ID: vg0506861028 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6861028
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, T: 0.10, others allele: 0.00, population size: 295. )

Flanking Sequence (100 bp) in Reference Genome:


AGGACTGCAATGAAGCCCTTAAGATTCAACCCAACTATTGGAAGGCTCTCCTAAGGCGTGCAGCTTCCTATGGCAAGGTAATACTTTGCTCAATCAAGAT[G/T]
CTTTTATGCACATGATGATTGATGCTGGAAGACTTATGTTGTGCACACTATTTGCTTCTTTGGTGATTAGATTGAACAATGGGCAGATTCCGTGAAAGAT

Reverse complement sequence

ATCTTTCACGGAATCTGCCCATTGTTCAATCTAATCACCAAAGAAGCAAATAGTGTGCACAACATAAGTCTTCCAGCATCAATCATCATGTGCATAAAAG[C/A]
ATCTTGATTGAGCAAAGTATTACCTTGCCATAGGAAGCTGCACGCCTTAGGAGAGCCTTCCAATAGTTGGGTTGAATCTTAAGGGCTTCATTGCAGTCCT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.30% 46.40% 0.28% 0.02% NA
All Indica  2759 83.90% 15.60% 0.43% 0.04% NA
All Japonica  1512 2.70% 97.30% 0.00% 0.00% NA
Aus  269 47.60% 52.40% 0.00% 0.00% NA
Indica I  595 92.60% 7.40% 0.00% 0.00% NA
Indica II  465 80.20% 19.40% 0.43% 0.00% NA
Indica III  913 84.20% 15.30% 0.44% 0.00% NA
Indica Intermediate  786 79.30% 19.80% 0.76% 0.13% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 4.20% 95.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 35.60% 63.30% 1.11% 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
vg0506861028 G -> T LOC_Os05g12000.1 downstream_gene_variant ; 2650.0bp to feature; MODIFIER silent_mutation Average:70.416; most accessible tissue: Callus, score: 81.032 N N N N
vg0506861028 G -> T LOC_Os05g11990.1 intron_variant ; MODIFIER silent_mutation Average:70.416; most accessible tissue: Callus, score: 81.032 N N N N
vg0506861028 G -> T LOC_Os05g11990.2 intron_variant ; MODIFIER silent_mutation Average:70.416; most accessible tissue: Callus, score: 81.032 N N N N
vg0506861028 G -> DEL N N silent_mutation Average:70.416; most accessible tissue: Callus, score: 81.032 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506861028 6.74E-11 4.00E-38 mr1039 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
vg0506861028 2.28E-09 1.57E-10 mr1039 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
vg0506861028 NA 5.91E-11 mr1514 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
vg0506861028 8.74E-06 3.87E-08 mr1593 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
vg0506861028 8.80E-08 1.55E-34 mr1632 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
vg0506861028 5.59E-08 1.82E-10 mr1632 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
vg0506861028 2.94E-07 4.90E-42 mr1873 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
vg0506861028 3.17E-06 1.97E-09 mr1873 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
vg0506861028 1.06E-13 2.27E-43 mr1039_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
vg0506861028 5.15E-10 1.49E-11 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
vg0506861028 1.21E-06 8.74E-17 mr1514_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
vg0506861028 NA 6.16E-06 mr1514_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
vg0506861028 NA 2.95E-08 mr1593_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
vg0506861028 9.89E-17 3.10E-54 mr1632_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
vg0506861028 1.47E-13 4.31E-16 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
vg0506861028 NA 3.19E-09 mr1835_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
vg0506861028 1.75E-10 4.13E-44 mr1873_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
vg0506861028 1.37E-07 2.44E-11 mr1873_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