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Detailed information for vg0211585441:

Variant ID: vg0211585441 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 11585441
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTCATATAGGTCTCTAAACTCTCAAAATACATATCCAGATCCTAAAACTTATCAAAGTGTATCATCTATGTCCCAAATCAACACATCCCCTCTAGGATT[C/A]
TACGTAACGCTGATATGGCATACCACATGGACATGACGTGATGTGTCCTTTTTTTCCATCTTTTCTTTTTCTTTTTCTTCTCATTCTTCTTTTTTTTTTC

Reverse complement sequence

GAAAAAAAAAAGAAGAATGAGAAGAAAAAGAAAAAGAAAAGATGGAAAAAAAGGACACATCACGTCATGTCCATGTGGTATGCCATATCAGCGTTACGTA[G/T]
AATCCTAGAGGGGATGTGTTGATTTGGGACATAGATGATACACTTTGATAAGTTTTAGGATCTGGATATGTATTTTGAGAGTTTAGAGACCTATATGACA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.60% 35.30% 0.11% 0.00% NA
All Indica  2759 98.40% 1.40% 0.14% 0.00% NA
All Japonica  1512 1.70% 98.30% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 97.60% 1.90% 0.43% 0.00% NA
Indica III  913 98.70% 1.20% 0.11% 0.00% NA
Indica Intermediate  786 97.60% 2.40% 0.00% 0.00% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 2.80% 97.20% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 98.30% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 46.70% 52.20% 1.11% 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
vg0211585441 C -> A LOC_Os02g19804.1 downstream_gene_variant ; 1850.0bp to feature; MODIFIER silent_mutation Average:46.132; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N
vg0211585441 C -> A LOC_Os02g19804-LOC_Os02g19820 intergenic_region ; MODIFIER silent_mutation Average:46.132; most accessible tissue: Minghui63 panicle, score: 66.554 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0211585441 4.04E-06 NA mr1267_2 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
vg0211585441 5.98E-06 5.98E-06 mr1267_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
vg0211585441 NA 2.67E-06 mr1329_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
vg0211585441 NA 2.78E-06 mr1754_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
vg0211585441 NA 2.99E-07 mr1982_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