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Detailed information for vg1100141408:

Variant ID: vg1100141408 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 141408
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.14, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TTAGGGTGCAAGACTTCCGTCGCGTCTGGGAACATCGCTTTAACAGCTAAGGGCATCCACAATGCTATTATTTGGTAATAAGTAATGCTACTACTTAACT[G/A]
CAGCAACTGTATGTCCCATGCGTTATACGGAGGGACCTATCCCAAGATATGCTCGCCCCGACGATGCCTTGCAGATCCTCTCTCTCCAAGTGATAGAAGC

Reverse complement sequence

GCTTCTATCACTTGGAGAGAGAGGATCTGCAAGGCATCGTCGGGGCGAGCATATCTTGGGATAGGTCCCTCCGTATAACGCATGGGACATACAGTTGCTG[C/T]
AGTTAAGTAGTAGCATTACTTATTACCAAATAATAGCATTGTGGATGCCCTTAGCTGTTAAAGCGATGTTCCCAGACGCGACGGAAGTCTTGCACCCTAA

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 52.20% 47.50% 0.23% 0.11% NA
All Indica  2759 84.80% 14.70% 0.33% 0.18% NA
All Japonica  1512 1.50% 98.50% 0.00% 0.00% NA
Aus  269 27.50% 72.50% 0.00% 0.00% NA
Indica I  595 97.60% 2.00% 0.17% 0.17% NA
Indica II  465 53.80% 45.60% 0.22% 0.43% NA
Indica III  913 92.60% 7.10% 0.33% 0.00% NA
Indica Intermediate  786 84.40% 14.90% 0.51% 0.25% NA
Temperate Japonica  767 1.40% 98.60% 0.00% 0.00% NA
Tropical Japonica  504 1.40% 98.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 22.20% 75.60% 2.22% 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
vg1100141408 G -> A LOC_Os11g01250.1 upstream_gene_variant ; 1090.0bp to feature; MODIFIER silent_mutation Average:68.648; most accessible tissue: Zhenshan97 flower, score: 87.106 N N N N
vg1100141408 G -> A LOC_Os11g01240.1 downstream_gene_variant ; 2449.0bp to feature; MODIFIER silent_mutation Average:68.648; most accessible tissue: Zhenshan97 flower, score: 87.106 N N N N
vg1100141408 G -> A LOC_Os11g01270.1 downstream_gene_variant ; 2757.0bp to feature; MODIFIER silent_mutation Average:68.648; most accessible tissue: Zhenshan97 flower, score: 87.106 N N N N
vg1100141408 G -> A LOC_Os11g01260.1 intron_variant ; MODIFIER silent_mutation Average:68.648; most accessible tissue: Zhenshan97 flower, score: 87.106 N N N N
vg1100141408 G -> DEL N N silent_mutation Average:68.648; most accessible tissue: Zhenshan97 flower, score: 87.106 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1100141408 NA 7.79E-06 mr1032 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
vg1100141408 NA 7.89E-06 mr1478 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
vg1100141408 NA 8.92E-12 mr1609 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
vg1100141408 NA 2.11E-10 mr1889 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
vg1100141408 NA 1.89E-08 mr1903 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
vg1100141408 NA 3.22E-14 mr1907 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
vg1100141408 NA 1.03E-09 mr1934 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
vg1100141408 NA 1.19E-08 mr1935 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
vg1100141408 NA 4.37E-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
vg1100141408 NA 8.99E-14 mr1889_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
vg1100141408 NA 6.26E-08 mr1896_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
vg1100141408 NA 3.24E-13 mr1907_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
vg1100141408 NA 5.61E-10 mr1934_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