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Detailed information for vg0225962935:

Variant ID: vg0225962935 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25962935
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGTTAACAAATATATGATTTTATTAAAGTATTTTTAAGACTAATTTATACATGTAGTCATCACATTTGATTGACAAATATTTTAAAAGTGATTCATAAT[C/T]
AAATATTCTAAAGTTTGACCTCACACTTGTCTAAAACGATAAGTATTATCAGCCCGGAAAAAGTAGTATTTATTTAGCACATCTCTAAACTCACCAAAAT

Reverse complement sequence

ATTTTGGTGAGTTTAGAGATGTGCTAAATAAATACTACTTTTTCCGGGCTGATAATACTTATCGTTTTAGACAAGTGTGAGGTCAAACTTTAGAATATTT[G/A]
ATTATGAATCACTTTTAAAATATTTGTCAATCAAATGTGATGACTACATGTATAAATTAGTCTTAAAAATACTTTAATAAAATCATATATTTGTTAACAC

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 82.90% 14.10% 3.00% 0.00% NA
All Indica  2759 98.90% 0.90% 0.22% 0.00% NA
All Japonica  1512 54.30% 40.30% 5.42% 0.00% NA
Aus  269 99.30% 0.40% 0.37% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 98.90% 0.80% 0.33% 0.00% NA
Indica Intermediate  786 97.80% 1.90% 0.25% 0.00% NA
Temperate Japonica  767 86.40% 11.10% 2.48% 0.00% NA
Tropical Japonica  504 12.50% 85.50% 1.98% 0.00% NA
Japonica Intermediate  241 39.40% 38.60% 21.99% 0.00% NA
VI/Aromatic  96 33.30% 18.80% 47.92% 0.00% NA
Intermediate  90 77.80% 14.40% 7.78% 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
vg0225962935 C -> T LOC_Os02g43110.1 upstream_gene_variant ; 3558.0bp to feature; MODIFIER silent_mutation Average:49.992; most accessible tissue: Zhenshan97 flower, score: 66.841 N N N N
vg0225962935 C -> T LOC_Os02g43120.1 downstream_gene_variant ; 4817.0bp to feature; MODIFIER silent_mutation Average:49.992; most accessible tissue: Zhenshan97 flower, score: 66.841 N N N N
vg0225962935 C -> T LOC_Os02g43110-LOC_Os02g43120 intergenic_region ; MODIFIER silent_mutation Average:49.992; most accessible tissue: Zhenshan97 flower, score: 66.841 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225962935 3.91E-06 3.91E-06 mr1228 Jap_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
vg0225962935 NA 1.04E-09 mr1533 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
vg0225962935 NA 7.93E-07 mr1606 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
vg0225962935 NA 2.42E-11 mr1980 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
vg0225962935 NA 7.09E-10 mr1338_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
vg0225962935 NA 1.53E-10 mr1379_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
vg0225962935 NA 1.29E-06 mr1379_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
vg0225962935 NA 1.62E-09 mr1905_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