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Detailed information for vg1112909023:

Variant ID: vg1112909023 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 12909023
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


CAATACTTCGTGACATGGGACCATCCAAACGGTCAACCGAACCGGCGAACGGAACCGACGGCTCAGACACGGTTTACGACAGAGACTCGGTACAGCAAGC[G/A]
ATAGGCCGGTAGGGGTTTAGGGATGCACCTATGGCTTTGCGACTCGGCTACTGAGCTACGGGCAGCGGCAAACCACGACAGCTAGGCGGTGACACAAGGC

Reverse complement sequence

GCCTTGTGTCACCGCCTAGCTGTCGTGGTTTGCCGCTGCCCGTAGCTCAGTAGCCGAGTCGCAAAGCCATAGGTGCATCCCTAAACCCCTACCGGCCTAT[C/T]
GCTTGCTGTACCGAGTCTCTGTCGTAAACCGTGTCTGAGCCGTCGGTTCCGTTCGCCGGTTCGGTTGACCGTTTGGATGGTCCCATGTCACGAAGTATTG

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 42.20% 31.50% 0.28% 26.01% NA
All Indica  2759 15.30% 41.80% 0.47% 42.44% NA
All Japonica  1512 95.50% 1.60% 0.00% 2.91% NA
Aus  269 0.00% 100.00% 0.00% 0.00% NA
Indica I  595 38.80% 19.50% 0.84% 40.84% NA
Indica II  465 9.90% 64.10% 0.43% 25.59% NA
Indica III  913 1.90% 41.40% 0.33% 56.41% NA
Indica Intermediate  786 16.20% 46.10% 0.38% 37.40% NA
Temperate Japonica  767 96.90% 2.10% 0.00% 1.04% NA
Tropical Japonica  504 92.50% 1.20% 0.00% 6.35% NA
Japonica Intermediate  241 97.50% 0.80% 0.00% 1.66% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 48.90% 35.60% 0.00% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1112909023 G -> A LOC_Os11g22460.1 upstream_gene_variant ; 1547.0bp to feature; MODIFIER silent_mutation Average:44.199; most accessible tissue: Zhenshan97 young leaf, score: 76.44 N N N N
vg1112909023 G -> A LOC_Os11g22449.1 downstream_gene_variant ; 3530.0bp to feature; MODIFIER silent_mutation Average:44.199; most accessible tissue: Zhenshan97 young leaf, score: 76.44 N N N N
vg1112909023 G -> A LOC_Os11g22460-LOC_Os11g22470 intergenic_region ; MODIFIER silent_mutation Average:44.199; most accessible tissue: Zhenshan97 young leaf, score: 76.44 N N N N
vg1112909023 G -> DEL N N silent_mutation Average:44.199; most accessible tissue: Zhenshan97 young leaf, score: 76.44 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1112909023 8.55E-06 NA mr1053 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
vg1112909023 1.44E-06 NA mr1067 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
vg1112909023 2.03E-06 NA mr1067 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
vg1112909023 NA 2.86E-06 mr1069 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
vg1112909023 NA 6.78E-06 mr1075 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
vg1112909023 2.54E-06 NA mr1077 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
vg1112909023 3.57E-06 3.15E-10 mr1077 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
vg1112909023 2.72E-06 NA mr1080 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
vg1112909023 NA 2.14E-06 mr1149 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
vg1112909023 NA 1.62E-06 mr1277 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
vg1112909023 NA 2.55E-09 mr1302 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
vg1112909023 NA 1.55E-06 mr1315 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
vg1112909023 NA 4.82E-06 mr1418 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
vg1112909023 NA 4.51E-08 mr1420 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
vg1112909023 NA 1.85E-07 mr1424 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
vg1112909023 NA 6.29E-06 mr1507 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
vg1112909023 NA 1.45E-06 mr1646 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
vg1112909023 NA 8.09E-09 mr1659 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
vg1112909023 NA 4.99E-06 mr1758 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
vg1112909023 NA 2.74E-07 mr1764 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
vg1112909023 NA 5.07E-06 mr1771 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
vg1112909023 3.29E-08 NA mr1795 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
vg1112909023 1.41E-08 1.99E-08 mr1795 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
vg1112909023 NA 2.07E-06 mr1884 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
vg1112909023 NA 4.50E-12 mr1921 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
vg1112909023 NA 1.02E-06 mr1962 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