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Detailed information for vg0141059016:

Variant ID: vg0141059016 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41059016
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


ATCACCGCCGTCCATTCTGAATTGGTAACTACTGTACCAATTAGCGACAGTTCAAAATTAGTTGCATAATTTCTGTCTTGTTTGGAGATGACTCTGCGTC[G/A]
GACATCCGATATTCCATCAAATATCGGACGCATGATGTTTGCGTGTCATCACACCACCTGCGTATGCAGCATGACCAAAAAAAAATTGGTCCGTCAAATG

Reverse complement sequence

CATTTGACGGACCAATTTTTTTTTGGTCATGCTGCATACGCAGGTGGTGTGATGACACGCAAACATCATGCGTCCGATATTTGATGGAATATCGGATGTC[C/T]
GACGCAGAGTCATCTCCAAACAAGACAGAAATTATGCAACTAATTTTGAACTGTCGCTAATTGGTACAGTAGTTACCAATTCAGAATGGACGGCGGTGAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.60% 47.30% 0.06% 0.00% NA
All Indica  2759 21.50% 78.50% 0.04% 0.00% NA
All Japonica  1512 98.10% 1.80% 0.07% 0.00% NA
Aus  269 96.30% 3.70% 0.00% 0.00% NA
Indica I  595 15.10% 84.90% 0.00% 0.00% NA
Indica II  465 2.80% 97.20% 0.00% 0.00% NA
Indica III  913 30.30% 69.60% 0.11% 0.00% NA
Indica Intermediate  786 27.00% 73.00% 0.00% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 97.20% 2.60% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 63.30% 35.60% 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
vg0141059016 G -> A LOC_Os01g70930.1 upstream_gene_variant ; 144.0bp to feature; MODIFIER silent_mutation Average:78.87; most accessible tissue: Callus, score: 89.019 N N N N
vg0141059016 G -> A LOC_Os01g70940.1 upstream_gene_variant ; 2075.0bp to feature; MODIFIER silent_mutation Average:78.87; most accessible tissue: Callus, score: 89.019 N N N N
vg0141059016 G -> A LOC_Os01g70940.2 upstream_gene_variant ; 2075.0bp to feature; MODIFIER silent_mutation Average:78.87; most accessible tissue: Callus, score: 89.019 N N N N
vg0141059016 G -> A LOC_Os01g70940.3 upstream_gene_variant ; 2075.0bp to feature; MODIFIER silent_mutation Average:78.87; most accessible tissue: Callus, score: 89.019 N N N N
vg0141059016 G -> A LOC_Os01g70920.1 downstream_gene_variant ; 2367.0bp to feature; MODIFIER silent_mutation Average:78.87; most accessible tissue: Callus, score: 89.019 N N N N
vg0141059016 G -> A LOC_Os01g70920.2 downstream_gene_variant ; 2367.0bp to feature; MODIFIER silent_mutation Average:78.87; most accessible tissue: Callus, score: 89.019 N N N N
vg0141059016 G -> A LOC_Os01g70920.3 downstream_gene_variant ; 2367.0bp to feature; MODIFIER silent_mutation Average:78.87; most accessible tissue: Callus, score: 89.019 N N N N
vg0141059016 G -> A LOC_Os01g70930-LOC_Os01g70940 intergenic_region ; MODIFIER silent_mutation Average:78.87; most accessible tissue: Callus, score: 89.019 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141059016 NA 3.14E-20 mr1244 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
vg0141059016 NA 5.10E-11 mr1457 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
vg0141059016 NA 6.05E-51 mr1458 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
vg0141059016 NA 2.38E-07 mr1458 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
vg0141059016 NA 5.02E-06 mr1027_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
vg0141059016 NA 1.30E-49 mr1063_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
vg0141059016 NA 6.23E-22 mr1164_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
vg0141059016 NA 2.11E-15 mr1180_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
vg0141059016 NA 8.75E-21 mr1183_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
vg0141059016 NA 1.72E-07 mr1215_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
vg0141059016 NA 2.48E-21 mr1218_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
vg0141059016 NA 6.73E-09 mr1220_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
vg0141059016 NA 8.48E-35 mr1221_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
vg0141059016 NA 3.48E-24 mr1244_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
vg0141059016 NA 1.04E-16 mr1260_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
vg0141059016 NA 7.00E-09 mr1319_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
vg0141059016 NA 1.91E-08 mr1322_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
vg0141059016 NA 2.60E-28 mr1323_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
vg0141059016 NA 1.60E-13 mr1330_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
vg0141059016 NA 2.42E-17 mr1352_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
vg0141059016 NA 5.15E-24 mr1422_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
vg0141059016 NA 2.03E-18 mr1454_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
vg0141059016 NA 9.92E-07 mr1454_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
vg0141059016 NA 1.39E-19 mr1457_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
vg0141059016 NA 1.13E-58 mr1458_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
vg0141059016 NA 1.32E-09 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
vg0141059016 NA 1.09E-08 mr1527_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
vg0141059016 NA 6.03E-30 mr1580_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
vg0141059016 NA 5.23E-11 mr1781_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
vg0141059016 NA 3.87E-68 mr1798_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
vg0141059016 NA 5.90E-30 mr1825_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
vg0141059016 4.61E-06 NA mr1875_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
vg0141059016 NA 4.09E-07 mr1875_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
vg0141059016 9.88E-07 NA mr1908_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
vg0141059016 NA 3.88E-07 mr1908_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