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Detailed information for vg0808423022:

Variant ID: vg0808423022 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 8423022
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


TACATCAGTGAGAATTCCTAATGCTTACCAATTGCTGCATCTTGATTGCAAGCTCCAGAAAAAAATATTGTCATGATTATTGTGCCAGGGGGAGAAGTTT[C/T]
GGTTTTTTATGTGTTTTGTATGAGACCAGTGCAAGGGGATCTACATTGTTCTGGATTTTGTTTTGGTTTCAATTTTGCTGGTCCTACTACGTGTGCATAT

Reverse complement sequence

ATATGCACACGTAGTAGGACCAGCAAAATTGAAACCAAAACAAAATCCAGAACAATGTAGATCCCCTTGCACTGGTCTCATACAAAACACATAAAAAACC[G/A]
AAACTTCTCCCCCTGGCACAATAATCATGACAATATTTTTTTCTGGAGCTTGCAATCAAGATGCAGCAATTGGTAAGCATTAGGAATTCTCACTGATGTA

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 74.00% 26.00% 0.06% 0.00% NA
All Indica  2759 67.90% 32.10% 0.07% 0.00% NA
All Japonica  1512 90.80% 9.20% 0.00% 0.00% NA
Aus  269 39.00% 60.60% 0.37% 0.00% NA
Indica I  595 45.70% 54.10% 0.17% 0.00% NA
Indica II  465 84.10% 15.90% 0.00% 0.00% NA
Indica III  913 74.80% 25.20% 0.00% 0.00% NA
Indica Intermediate  786 66.90% 33.00% 0.13% 0.00% NA
Temperate Japonica  767 99.10% 0.90% 0.00% 0.00% NA
Tropical Japonica  504 81.30% 18.70% 0.00% 0.00% NA
Japonica Intermediate  241 84.20% 15.80% 0.00% 0.00% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg0808423022 C -> T LOC_Os08g14050.1 upstream_gene_variant ; 4457.0bp to feature; MODIFIER silent_mutation Average:45.437; most accessible tissue: Callus, score: 67.217 N N N N
vg0808423022 C -> T LOC_Os08g14070.1 upstream_gene_variant ; 1262.0bp to feature; MODIFIER silent_mutation Average:45.437; most accessible tissue: Callus, score: 67.217 N N N N
vg0808423022 C -> T LOC_Os08g14050-LOC_Os08g14070 intergenic_region ; MODIFIER silent_mutation Average:45.437; most accessible tissue: Callus, score: 67.217 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0808423022 NA 8.70E-11 Heading_date Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0808423022 NA 5.46E-07 mr1583 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
vg0808423022 NA 1.84E-06 mr1038_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
vg0808423022 NA 5.75E-07 mr1092_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
vg0808423022 NA 1.07E-07 mr1097_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
vg0808423022 NA 4.65E-09 mr1125_2 Ind_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
vg0808423022 NA 1.21E-08 mr1152_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
vg0808423022 NA 5.55E-07 mr1154_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
vg0808423022 NA 3.50E-06 mr1215_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
vg0808423022 NA 4.57E-06 mr1220_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
vg0808423022 NA 3.99E-06 mr1553_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
vg0808423022 NA 2.18E-06 mr1566_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
vg0808423022 NA 3.41E-06 mr1924_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