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Detailed information for vg1122937279:

Variant ID: vg1122937279 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22937279
Reference Allele: CAlternative Allele: G,T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAATGATTGAATCCTATCCACTACTCTATTTCTCCTAAATATTCCCATGTTATTTATGTAAACAGCTGACAACTACGTACTAACATACTCCCTCAATCC[C/G,T]
ATAAAAAACCAACCTAATACTACATGTAACATATCCTACTACTACGAATCTAGACATACATATGTATCCAGATTCATCGTATTAGAATATGTCATATCCG

Reverse complement sequence

CGGATATGACATATTCTAATACGATGAATCTGGATACATATGTATGTCTAGATTCGTAGTAGTAGGATATGTTACATGTAGTATTAGGTTGGTTTTTTAT[G/C,A]
GGATTGAGGGAGTATGTTAGTACGTAGTTGTCAGCTGTTTACATAAATAACATGGGAATATTTAGGAGAAATAGAGTAGTGGATAGGATTCAATCATTCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.40% 5.80% 0.17% 0.00% G: 2.67%
All Indica  2759 90.90% 4.70% 0.11% 0.00% G: 4.24%
All Japonica  1512 91.50% 8.10% 0.33% 0.00% G: 0.13%
Aus  269 94.10% 5.60% 0.00% 0.00% G: 0.37%
Indica I  595 93.60% 6.20% 0.00% 0.00% G: 0.17%
Indica II  465 96.80% 1.90% 0.00% 0.00% G: 1.29%
Indica III  913 87.10% 5.10% 0.22% 0.00% G: 7.56%
Indica Intermediate  786 89.90% 4.70% 0.13% 0.00% G: 5.22%
Temperate Japonica  767 98.60% 1.30% 0.00% 0.00% G: 0.13%
Tropical Japonica  504 79.20% 20.00% 0.79% 0.00% NA
Japonica Intermediate  241 94.60% 4.60% 0.41% 0.00% G: 0.41%
VI/Aromatic  96 96.90% 0.00% 0.00% 0.00% G: 3.12%
Intermediate  90 90.00% 6.70% 0.00% 0.00% G: 3.33%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122937279 C -> T LOC_Os11g38660.1 downstream_gene_variant ; 4301.0bp to feature; MODIFIER silent_mutation Average:70.324; most accessible tissue: Callus, score: 90.317 N N N N
vg1122937279 C -> T LOC_Os11g38650-LOC_Os11g38660 intergenic_region ; MODIFIER silent_mutation Average:70.324; most accessible tissue: Callus, score: 90.317 N N N N
vg1122937279 C -> G LOC_Os11g38660.1 downstream_gene_variant ; 4301.0bp to feature; MODIFIER silent_mutation Average:70.324; most accessible tissue: Callus, score: 90.317 N N N N
vg1122937279 C -> G LOC_Os11g38650-LOC_Os11g38660 intergenic_region ; MODIFIER silent_mutation Average:70.324; most accessible tissue: Callus, score: 90.317 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122937279 NA 1.43E-07 mr1422 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
vg1122937279 NA 1.46E-09 mr1583 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
vg1122937279 NA 1.01E-06 mr1970 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
vg1122937279 NA 3.70E-08 mr1973 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
vg1122937279 NA 7.61E-06 mr1124_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
vg1122937279 NA 2.47E-06 mr1218_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
vg1122937279 2.88E-06 1.68E-09 mr1422_2 Jap_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
vg1122937279 5.11E-07 1.45E-09 mr1583_2 Jap_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
vg1122937279 3.93E-09 NA mr1850_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
vg1122937279 1.33E-12 5.86E-17 mr1850_2 Jap_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
vg1122937279 NA 3.78E-07 mr1970_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
vg1122937279 NA 2.73E-09 mr1973_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