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Detailed information for vg0102576228:

Variant ID: vg0102576228 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2576228
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTGTTTCCATATGTTACTCTGTTTCCATGCTCTCAACTGATAGGTTCCTCAAATAATAAGAAAACAATCAATCATCAATAAGATATAATGGAGCAGTC[C/T]
ACTCCAACACTGTAAAATTTTGTCACCCGGTTGACCAGTAGGGAAAAAAGAAAACAGTTGTGAGTACAGCAAATTGAATTCTGCCTTCACCATATTGGTC

Reverse complement sequence

GACCAATATGGTGAAGGCAGAATTCAATTTGCTGTACTCACAACTGTTTTCTTTTTTCCCTACTGGTCAACCGGGTGACAAAATTTTACAGTGTTGGAGT[G/A]
GACTGCTCCATTATATCTTATTGATGATTGATTGTTTTCTTATTATTTGAGGAACCTATCAGTTGAGAGCATGGAAACAGAGTAACATATGGAAACAATC

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 90.30% 9.70% 0.00% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 71.40% 28.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 52.40% 47.60% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 74.70% 25.30% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0102576228 C -> T LOC_Os01g05440.1 upstream_gene_variant ; 4231.0bp to feature; MODIFIER silent_mutation Average:56.387; most accessible tissue: Callus, score: 87.437 N N N N
vg0102576228 C -> T LOC_Os01g05450.1 upstream_gene_variant ; 2027.0bp to feature; MODIFIER silent_mutation Average:56.387; most accessible tissue: Callus, score: 87.437 N N N N
vg0102576228 C -> T LOC_Os01g05470.1 downstream_gene_variant ; 3324.0bp to feature; MODIFIER silent_mutation Average:56.387; most accessible tissue: Callus, score: 87.437 N N N N
vg0102576228 C -> T LOC_Os01g05460.1 intron_variant ; MODIFIER silent_mutation Average:56.387; most accessible tissue: Callus, score: 87.437 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102576228 4.95E-07 NA Grain_thickness All YES 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
vg0102576228 NA 4.59E-06 mr1461 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
vg0102576228 NA 8.85E-06 mr1621_2 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