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Detailed information for vg1121209742:

Variant ID: vg1121209742 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21209742
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.10, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


GATGGCGCCCCGCGATGCCGCTACTTCTTATGGTTGGTTGCTCTCAACAGGTGCTGGATCGTGGACCTCCTCCACAACCGTGGCCTCCCACACCTAGACC[G/A]
TTGCGTCATTTGTGATCAACACGAAGAGAGCATAGAACGTGGCTAGAGGTTGCGAAGGCAATGATTGCTGAAGCGGAACTCTGGCGTTTGGCCAACGCGG

Reverse complement sequence

CCGCGTTGGCCAAACGCCAGAGTTCCGCTTCAGCAATCATTGCCTTCGCAACCTCTAGCCACGTTCTATGCTCTCTTCGTGTTGATCACAAATGACGCAA[C/T]
GGTCTAGGTGTGGGAGGCCACGGTTGTGGAGGAGGTCCACGATCCAGCACCTGTTGAGAGCAACCAACCATAAGAAGTAGCGGCATCGCGGGGCGCCATC

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 58.20% 40.80% 0.30% 0.74% NA
All Indica  2759 59.00% 40.40% 0.29% 0.29% NA
All Japonica  1512 51.90% 47.80% 0.20% 0.07% NA
Aus  269 70.30% 20.80% 0.00% 8.92% NA
Indica I  595 32.60% 67.40% 0.00% 0.00% NA
Indica II  465 68.20% 31.20% 0.65% 0.00% NA
Indica III  913 67.60% 31.70% 0.22% 0.55% NA
Indica Intermediate  786 63.70% 35.50% 0.38% 0.38% NA
Temperate Japonica  767 21.40% 78.50% 0.13% 0.00% NA
Tropical Japonica  504 86.30% 13.30% 0.40% 0.00% NA
Japonica Intermediate  241 77.20% 22.40% 0.00% 0.41% NA
VI/Aromatic  96 96.90% 2.10% 0.00% 1.04% NA
Intermediate  90 58.90% 36.70% 3.33% 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
vg1121209742 G -> A LOC_Os11g36070.1 downstream_gene_variant ; 2415.0bp to feature; MODIFIER silent_mutation Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg1121209742 G -> A LOC_Os11g36090.1 downstream_gene_variant ; 969.0bp to feature; MODIFIER silent_mutation Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg1121209742 G -> A LOC_Os11g36070.4 downstream_gene_variant ; 2415.0bp to feature; MODIFIER silent_mutation Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg1121209742 G -> A LOC_Os11g36070.3 downstream_gene_variant ; 2415.0bp to feature; MODIFIER silent_mutation Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg1121209742 G -> A LOC_Os11g36070.2 downstream_gene_variant ; 2415.0bp to feature; MODIFIER silent_mutation Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg1121209742 G -> A LOC_Os11g36070-LOC_Os11g36090 intergenic_region ; MODIFIER silent_mutation Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N
vg1121209742 G -> DEL N N silent_mutation Average:68.191; most accessible tissue: Zhenshan97 young leaf, score: 87.004 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121209742 NA 5.93E-06 mr1013 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
vg1121209742 NA 3.43E-06 mr1034 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
vg1121209742 NA 3.88E-07 mr1291 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
vg1121209742 NA 1.16E-06 mr1324 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
vg1121209742 NA 7.56E-09 mr1502 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
vg1121209742 NA 5.20E-06 mr1502 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
vg1121209742 NA 1.61E-07 mr1543 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
vg1121209742 1.73E-06 NA mr1580 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
vg1121209742 NA 1.01E-06 mr1729 Jap_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
vg1121209742 NA 5.24E-06 mr1808 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
vg1121209742 NA 2.06E-12 mr1879 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
vg1121209742 NA 3.45E-06 mr1892 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
vg1121209742 8.67E-06 8.66E-06 mr1966 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
vg1121209742 NA 3.81E-06 mr1986 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
vg1121209742 NA 6.33E-07 mr1042_2 Jap_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
vg1121209742 NA 5.75E-07 mr1274_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