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Detailed information for vg0108147243:

Variant ID: vg0108147243 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8147243
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, C: 0.04, T: 0.03, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


ATTAGTTTCATTAAATCAATAACTGAATATATTTTCACAATAAATCTATCTTAGGTTAAAAATATTATTATTTTTCTCTACAAACTTAATCAAACTTGAA[G/C]
CAATTTAACTTTGACCGAAAGATACTAATATTATTCTACATCGTCATCAAACTCTCAAGTAAATCATGTAAGTGTAAATATATACCCCATGGCAAGGACG

Reverse complement sequence

CGTCCTTGCCATGGGGTATATATTTACACTTACATGATTTACTTGAGAGTTTGATGACGATGTAGAATAATATTAGTATCTTTCGGTCAAAGTTAAATTG[C/G]
TTCAAGTTTGATTAAGTTTGTAGAGAAAAATAATAATATTTTTAACCTAAGATAGATTTATTGTGAAAATATATTCAGTTATTGATTTAATGAAACTAAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.30% 37.90% 5.84% 0.00% NA
All Indica  2759 84.00% 8.10% 7.87% 0.00% NA
All Japonica  1512 15.10% 81.50% 3.37% 0.00% NA
Aus  269 3.30% 96.30% 0.37% 0.00% NA
Indica I  595 70.90% 8.10% 21.01% 0.00% NA
Indica II  465 88.60% 4.30% 7.10% 0.00% NA
Indica III  913 90.70% 9.00% 0.33% 0.00% NA
Indica Intermediate  786 83.50% 9.40% 7.12% 0.00% NA
Temperate Japonica  767 2.90% 94.70% 2.48% 0.00% NA
Tropical Japonica  504 30.80% 64.30% 4.96% 0.00% NA
Japonica Intermediate  241 21.20% 75.90% 2.90% 0.00% NA
VI/Aromatic  96 51.00% 47.90% 1.04% 0.00% NA
Intermediate  90 63.30% 30.00% 6.67% 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
vg0108147243 G -> C LOC_Os01g14530.1 intron_variant ; MODIFIER silent_mutation Average:54.302; most accessible tissue: Zhenshan97 panicle, score: 76.605 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0108147243 7.67E-08 NA mr1134 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
vg0108147243 2.82E-07 1.84E-08 mr1134 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
vg0108147243 6.99E-09 NA mr1135 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
vg0108147243 1.49E-06 1.05E-07 mr1135 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
vg0108147243 7.55E-08 NA mr1504 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
vg0108147243 6.71E-07 1.38E-08 mr1504 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
vg0108147243 3.79E-07 NA mr1672 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
vg0108147243 NA 2.72E-07 mr1672 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
vg0108147243 NA 5.27E-31 mr1745 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
vg0108147243 NA 3.39E-18 mr1913 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