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Detailed information for vg1124303986:

Variant ID: vg1124303986 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24303986
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, C: 0.07, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


AAGTTTGACTAAGTTTACAGATAAATATAGTAATATTTATAATACTAAATTAGTTTCATCAAATCAATAATTGAATATATTTTTATAATAAATTTGTCTT[G/C]
GGTTGAAAATGCTACTACCTTTTTTATAAACTTGGTCAAACTTAAAGCCATTTGACTTTAACCAAAATCAAAACATATTATAACCTGAAACGGACGGAGT

Reverse complement sequence

ACTCCGTCCGTTTCAGGTTATAATATGTTTTGATTTTGGTTAAAGTCAAATGGCTTTAAGTTTGACCAAGTTTATAAAAAAGGTAGTAGCATTTTCAACC[C/G]
AAGACAAATTTATTATAAAAATATATTCAATTATTGATTTGATGAAACTAATTTAGTATTATAAATATTACTATATTTATCTGTAAACTTAGTCAAACTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.00% 33.90% 0.11% 0.00% NA
All Indica  2759 58.10% 41.90% 0.04% 0.00% NA
All Japonica  1512 75.10% 24.70% 0.20% 0.00% NA
Aus  269 90.00% 10.00% 0.00% 0.00% NA
Indica I  595 35.30% 64.70% 0.00% 0.00% NA
Indica II  465 53.50% 46.20% 0.22% 0.00% NA
Indica III  913 75.80% 24.20% 0.00% 0.00% NA
Indica Intermediate  786 57.40% 42.60% 0.00% 0.00% NA
Temperate Japonica  767 87.90% 11.90% 0.26% 0.00% NA
Tropical Japonica  504 68.30% 31.50% 0.20% 0.00% NA
Japonica Intermediate  241 48.50% 51.50% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 57.80% 41.10% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1124303986 G -> C LOC_Os11g40690.1 intron_variant ; MODIFIER silent_mutation Average:25.384; most accessible tissue: Callus, score: 41.173 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124303986 NA 9.33E-06 mr1040_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
vg1124303986 NA 8.28E-08 mr1045_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
vg1124303986 NA 1.25E-06 mr1053_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
vg1124303986 NA 4.31E-06 mr1238_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
vg1124303986 NA 2.42E-06 mr1318_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
vg1124303986 NA 7.55E-09 mr1609_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
vg1124303986 NA 7.16E-07 mr1735_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
vg1124303986 NA 7.44E-06 mr1763_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
vg1124303986 NA 6.32E-09 mr1788_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
vg1124303986 NA 1.20E-06 mr1795_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
vg1124303986 NA 9.84E-06 mr1900_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