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Detailed information for vg1125566004:

Variant ID: vg1125566004 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25566004
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TTATATAGAAAATCTTTAGTCTACCAACATTGTAAATAAAAATCAACAATCTTGATCTAGTCCGTGTATCCAAACTAACAAACTAACTTTGCTTCTCGAT[C/T]
GTTACAAAATAATTCATAATTACTATAGATGGAAGTTGATAAAGTATATGCGTTTGTAATGAGAAATGATTGTTGAGATGTTTGTGATGAGTCTGTTTGA

Reverse complement sequence

TCAAACAGACTCATCACAAACATCTCAACAATCATTTCTCATTACAAACGCATATACTTTATCAACTTCCATCTATAGTAATTATGAATTATTTTGTAAC[G/A]
ATCGAGAAGCAAAGTTAGTTTGTTAGTTTGGATACACGGACTAGATCAAGATTGTTGATTTTTATTTACAATGTTGGTAGACTAAAGATTTTCTATATAA

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 79.10% 20.00% 0.11% 0.87% NA
All Indica  2759 66.80% 32.90% 0.07% 0.18% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 82.90% 3.70% 0.37% 13.01% NA
Indica I  595 92.90% 6.90% 0.00% 0.17% NA
Indica II  465 80.20% 19.80% 0.00% 0.00% NA
Indica III  913 43.30% 56.40% 0.11% 0.22% NA
Indica Intermediate  786 66.40% 33.20% 0.13% 0.25% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 81.10% 15.60% 2.22% 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
vg1125566004 C -> T LOC_Os11g42450-LOC_Os11g42470 intergenic_region ; MODIFIER silent_mutation Average:25.271; most accessible tissue: Callus, score: 57.769 N N N N
vg1125566004 C -> DEL N N silent_mutation Average:25.271; most accessible tissue: Callus, score: 57.769 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125566004 4.26E-06 NA mr1133 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
vg1125566004 1.78E-07 5.34E-14 mr1133 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
vg1125566004 4.56E-09 2.70E-12 mr1191 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
vg1125566004 2.63E-06 7.69E-07 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
vg1125566004 3.39E-16 1.66E-18 mr1644 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
vg1125566004 2.13E-12 5.26E-12 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
vg1125566004 NA 1.34E-08 mr1662 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
vg1125566004 NA 1.82E-09 mr1662 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
vg1125566004 NA 5.50E-06 mr1667 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
vg1125566004 NA 1.83E-15 mr1133_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
vg1125566004 NA 5.14E-11 mr1133_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
vg1125566004 5.35E-10 NA mr1191_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
vg1125566004 1.19E-07 1.67E-06 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
vg1125566004 NA 1.78E-06 mr1662_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
vg1125566004 NA 4.86E-08 mr1662_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
vg1125566004 NA 3.54E-06 mr1667_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