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Detailed information for vg1126346197:

Variant ID: vg1126346197 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26346197
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, C: 0.37, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


ATAGTAAGTAAAACACTATAAAATGTAAAAAAATAATTATATGTGCACATACTTTGTCCCATTCGACTTTCTCTTCTTCTCCTATCTCACTCAACTCCTC[C/T]
GTCTTACAATTTTTAACTAATTAACAACATAATAAAAAATGATCAATAATTACAAAGCTAAATAATTATGATTCTTATCTCATATCTGTTTTTTAGCTTA

Reverse complement sequence

TAAGCTAAAAAACAGATATGAGATAAGAATCATAATTATTTAGCTTTGTAATTATTGATCATTTTTTATTATGTTGTTAATTAGTTAAAAATTGTAAGAC[G/A]
GAGGAGTTGAGTGAGATAGGAGAAGAAGAGAAAGTCGAATGGGACAAAGTATGTGCACATATAATTATTTTTTTACATTTTATAGTGTTTTACTTACTAT

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 53.30% 40.50% 4.30% 1.97% NA
All Indica  2759 48.30% 45.60% 3.62% 2.54% NA
All Japonica  1512 62.90% 30.80% 5.42% 0.93% NA
Aus  269 32.70% 58.70% 5.95% 2.60% NA
Indica I  595 72.80% 25.90% 1.01% 0.34% NA
Indica II  465 30.30% 67.30% 2.15% 0.22% NA
Indica III  913 36.50% 51.50% 5.70% 6.35% NA
Indica Intermediate  786 54.10% 40.70% 4.07% 1.15% NA
Temperate Japonica  767 84.40% 15.30% 0.39% 0.00% NA
Tropical Japonica  504 32.70% 49.60% 15.08% 2.58% NA
Japonica Intermediate  241 57.70% 40.70% 1.24% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 56.70% 35.60% 5.56% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126346197 C -> T LOC_Os11g43660.1 upstream_gene_variant ; 4589.0bp to feature; MODIFIER silent_mutation Average:28.089; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg1126346197 C -> T LOC_Os11g43650-LOC_Os11g43660 intergenic_region ; MODIFIER silent_mutation Average:28.089; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg1126346197 C -> DEL N N silent_mutation Average:28.089; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126346197 NA 2.62E-06 mr1191 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
vg1126346197 1.29E-06 9.53E-09 mr1295 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
vg1126346197 8.24E-07 4.05E-09 mr1644 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
vg1126346197 NA 1.13E-10 mr1769 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
vg1126346197 NA 2.88E-06 mr1158_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
vg1126346197 2.98E-07 5.99E-13 mr1191_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
vg1126346197 NA 1.14E-07 mr1330_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
vg1126346197 NA 1.15E-06 mr1336_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
vg1126346197 NA 1.31E-06 mr1380_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
vg1126346197 NA 4.01E-06 mr1561_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
vg1126346197 NA 5.21E-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
vg1126346197 NA 2.78E-06 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