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Detailed information for vg0323724850:

Variant ID: vg0323724850 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 23724850
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


CACGCCGGTCTGACCGGCTACCAGAGCCCGGTCTGACCGGTCACATAAAATGACGAATCCTACAATCACCTGTGAAATCTAATCATCTCCAAAACCACTT[C/T]
GTGAATAAATTCCAAATAACAAAACCAATAATCTCCAATGCCCAATTGTTCATCATAAAATAATAATCAAAAACACCTTTGATTTTACATTTTTTTCTCT

Reverse complement sequence

AGAGAAAAAAATGTAAAATCAAAGGTGTTTTTGATTATTATTTTATGATGAACAATTGGGCATTGGAGATTATTGGTTTTGTTATTTGGAATTTATTCAC[G/A]
AAGTGGTTTTGGAGATGATTAGATTTCACAGGTGATTGTAGGATTCGTCATTTTATGTGACCGGTCAGACCGGGCTCTGGTAGCCGGTCAGACCGGCGTG

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 94.20% 5.80% 0.02% 0.00% NA
All Indica  2759 90.10% 9.90% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 75.00% 25.00% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 96.10% 3.90% 0.00% 0.00% NA
Indica Intermediate  786 90.30% 9.50% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0323724850 C -> T LOC_Os03g42610.1 upstream_gene_variant ; 1117.0bp to feature; MODIFIER silent_mutation Average:36.932; most accessible tissue: Minghui63 flag leaf, score: 46.761 N N N N
vg0323724850 C -> T LOC_Os03g42610-LOC_Os03g42630 intergenic_region ; MODIFIER silent_mutation Average:36.932; most accessible tissue: Minghui63 flag leaf, score: 46.761 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0323724850 NA 2.68E-07 Spikelet_length 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
vg0323724850 NA 1.67E-06 mr1106 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
vg0323724850 NA 3.73E-06 mr1236 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
vg0323724850 1.90E-06 1.90E-06 mr1307 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
vg0323724850 NA 5.37E-06 mr1408 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
vg0323724850 NA 5.36E-07 mr1816 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
vg0323724850 NA 8.53E-06 mr1832 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