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Detailed information for vg0322468437:

Variant ID: vg0322468437 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 22468437
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


GAATGAATGTATATGAATGGGGGATGTTGGGGTGTGATATATCACGGCCTAGGGCTTAATAGGATTAATAGAATACTCATACCAACAAACTACAACTATT[C/T]
TTCCGGAAGCCGATCTTCAAATAACTTTGATATTAAGCGTGTTTAGCCTGGAGCAATTTCCTGATGGGTGACCGATTGGGAAGTGAACTTTGTGCAAAGT

Reverse complement sequence

ACTTTGCACAAAGTTCACTTCCCAATCGGTCACCCATCAGGAAATTGCTCCAGGCTAAACACGCTTAATATCAAAGTTATTTGAAGATCGGCTTCCGGAA[G/A]
AATAGTTGTAGTTTGTTGGTATGAGTATTCTATTAATCCTATTAAGCCCTAGGCCGTGATATATCACACCCCAACATCCCCCATTCATATACATTCATTC

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 92.30% 0.30% 3.45% 3.89% NA
All Indica  2759 87.00% 0.50% 5.84% 6.60% 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 55.60% 2.00% 19.16% 23.19% NA
Indica II  465 96.60% 0.20% 1.94% 1.29% NA
Indica III  913 99.90% 0.00% 0.00% 0.11% NA
Indica Intermediate  786 90.20% 0.30% 4.83% 4.71% 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 95.60% 0.00% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0322468437 C -> T LOC_Os03g40440.1 intron_variant ; MODIFIER silent_mutation Average:50.261; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0322468437 C -> DEL N N silent_mutation Average:50.261; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0322468437 NA 1.12E-06 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
vg0322468437 NA 7.11E-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
vg0322468437 5.01E-06 5.02E-06 mr1459 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
vg0322468437 1.79E-06 1.79E-06 mr1459 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