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Detailed information for vg0140952929:

Variant ID: vg0140952929 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 40952929
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.04, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGATTCCACTCCCGGCCAGATCTTCACCCGCGACGATGTCGACCTCCACCAATCCAACCGCCGCATCATCAGCCGAATATGCTGAGGTAAGTCCCCAT[T/C]
GGCTAGATCCCCTTTTCCGTTCATCAGACCGGTTTTCGCTCACCTTATCTTGTTTCCTTCTTCTCTATTCTTGTAGCATCTTTCCAATCTTGTTGCGGTT

Reverse complement sequence

AACCGCAACAAGATTGGAAAGATGCTACAAGAATAGAGAAGAAGGAAACAAGATAAGGTGAGCGAAAACCGGTCTGATGAACGGAAAAGGGGATCTAGCC[A/G]
ATGGGGACTTACCTCAGCATATTCGGCTGATGATGCGGCGGTTGGATTGGTGGAGGTCGACATCGTCGCGGGTGAAGATCTGGCCGGGAGTGGAATCGCC

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 62.70% 37.30% 0.02% 0.00% NA
All Indica  2759 97.30% 2.70% 0.00% 0.00% NA
All Japonica  1512 3.40% 96.60% 0.00% 0.00% NA
Aus  269 68.40% 31.20% 0.37% 0.00% NA
Indica I  595 97.60% 2.40% 0.00% 0.00% NA
Indica II  465 98.50% 1.50% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 1.80% 98.20% 0.00% 0.00% NA
Tropical Japonica  504 5.60% 94.40% 0.00% 0.00% NA
Japonica Intermediate  241 3.70% 96.30% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 44.40% 55.60% 0.00% 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
vg0140952929 T -> C LOC_Os01g70740.1 upstream_gene_variant ; 3336.0bp to feature; MODIFIER silent_mutation Average:30.971; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 N N N N
vg0140952929 T -> C LOC_Os01g70760.1 downstream_gene_variant ; 3426.0bp to feature; MODIFIER silent_mutation Average:30.971; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 N N N N
vg0140952929 T -> C LOC_Os01g70750.1 intron_variant ; MODIFIER silent_mutation Average:30.971; most accessible tissue: Zhenshan97 flag leaf, score: 53.034 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0140952929 NA 3.22E-28 mr1024 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
vg0140952929 8.71E-06 NA mr1135 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
vg0140952929 NA 1.70E-23 mr1375 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
vg0140952929 7.32E-06 NA mr1504 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
vg0140952929 NA 4.98E-06 mr1511 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
vg0140952929 NA 9.47E-08 mr1604 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
vg0140952929 NA 3.26E-08 mr1660 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
vg0140952929 6.39E-06 3.93E-37 mr1670 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
vg0140952929 NA 6.30E-07 mr1781 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
vg0140952929 NA 2.71E-26 mr1024_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
vg0140952929 NA 4.70E-09 mr1660_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
vg0140952929 3.53E-07 6.18E-50 mr1670_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
vg0140952929 NA 3.57E-11 mr1781_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