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Detailed information for vg0422582211:

Variant ID: vg0422582211 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 22582211
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTACAGGGATGCTACAGTAATCAGCCACTAATCATAGATTAATATATATCATTAGATTCGTCTCGCAAAATAGCCTAGGGGTTATGGAATCGGTTTTGT[C/T]
GGTAATCTATGTTTAATACTCCTAAATAGCAAGATTCCGGAGGGCTATTTAATAGTTCGGAGGATCCAAACAAGGCCATTGTTGATGTAGTACTCTGTAG

Reverse complement sequence

CTACAGAGTACTACATCAACAATGGCCTTGTTTGGATCCTCCGAACTATTAAATAGCCCTCCGGAATCTTGCTATTTAGGAGTATTAAACATAGATTACC[G/A]
ACAAAACCGATTCCATAACCCCTAGGCTATTTTGCGAGACGAATCTAATGATATATATTAATCTATGATTAGTGGCTGATTACTGTAGCATCCCTGTAGC

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 94.50% 3.80% 1.67% 0.00% NA
All Indica  2759 90.70% 6.40% 2.86% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 94.10% 0.20% 5.71% 0.00% NA
Indica II  465 85.20% 11.40% 3.44% 0.00% NA
Indica III  913 92.20% 7.10% 0.66% 0.00% NA
Indica Intermediate  786 89.70% 7.40% 2.93% 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
vg0422582211 C -> T LOC_Os04g37960.1 upstream_gene_variant ; 1245.0bp to feature; MODIFIER silent_mutation Average:61.294; most accessible tissue: Minghui63 flower, score: 81.696 N N N N
vg0422582211 C -> T LOC_Os04g37950-LOC_Os04g37960 intergenic_region ; MODIFIER silent_mutation Average:61.294; most accessible tissue: Minghui63 flower, score: 81.696 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0422582211 4.11E-07 NA mr1548 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
vg0422582211 1.93E-06 NA mr1548 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