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Detailed information for vg0203428380:

Variant ID: vg0203428380 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 3428380
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGTGTTCAACCCTAACTTCCAACTTTCCATCACATCACATCACATCCAAAACTTTCCTACACACATAAACTTCCAATTTTTTTTCCAAACTTCCAACTTT[C/T]
CCCAAACTTCCAACTTTTTTCAGGAACTAAACACAGCCTTAGTCTTATTAATCTAAATATCAAGGCCGACAAAAAGGAAAAGAATTATTTGATTCCAAGC

Reverse complement sequence

GCTTGGAATCAAATAATTCTTTTCCTTTTTGTCGGCCTTGATATTTAGATTAATAAGACTAAGGCTGTGTTTAGTTCCTGAAAAAAGTTGGAAGTTTGGG[G/A]
AAAGTTGGAAGTTTGGAAAAAAAATTGGAAGTTTATGTGTGTAGGAAAGTTTTGGATGTGATGTGATGTGATGGAAAGTTGGAAGTTAGGGTTGAACACA

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 37.80% 2.70% 23.36% 36.16% NA
All Indica  2759 20.70% 4.50% 38.42% 36.39% NA
All Japonica  1512 61.80% 0.10% 1.52% 36.57% NA
Aus  269 85.10% 0.00% 1.49% 13.38% NA
Indica I  595 12.60% 4.20% 44.03% 39.16% NA
Indica II  465 24.50% 0.40% 35.48% 39.57% NA
Indica III  913 23.20% 8.80% 36.80% 31.22% NA
Indica Intermediate  786 21.60% 2.20% 37.79% 38.42% NA
Temperate Japonica  767 70.40% 0.00% 0.91% 28.68% NA
Tropical Japonica  504 55.80% 0.20% 2.18% 41.87% NA
Japonica Intermediate  241 47.30% 0.00% 2.07% 50.62% NA
VI/Aromatic  96 6.20% 0.00% 1.04% 92.71% NA
Intermediate  90 51.10% 1.10% 17.78% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0203428380 C -> T LOC_Os02g06779.1 upstream_gene_variant ; 4934.0bp to feature; MODIFIER silent_mutation Average:13.355; most accessible tissue: Callus, score: 58.161 N N N N
vg0203428380 C -> T LOC_Os02g06790.1 downstream_gene_variant ; 167.0bp to feature; MODIFIER silent_mutation Average:13.355; most accessible tissue: Callus, score: 58.161 N N N N
vg0203428380 C -> T LOC_Os02g06779-LOC_Os02g06790 intergenic_region ; MODIFIER silent_mutation Average:13.355; most accessible tissue: Callus, score: 58.161 N N N N
vg0203428380 C -> DEL N N silent_mutation Average:13.355; most accessible tissue: Callus, score: 58.161 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0203428380 NA 5.34E-10 mr1201 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
vg0203428380 NA 7.27E-11 mr1201 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
vg0203428380 NA 4.84E-07 mr1219 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
vg0203428380 NA 4.14E-09 mr1219 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
vg0203428380 NA 3.17E-10 mr1274 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
vg0203428380 NA 1.98E-09 mr1274 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
vg0203428380 7.49E-06 3.95E-14 mr1201_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
vg0203428380 3.30E-06 3.38E-15 mr1201_2 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
vg0203428380 NA 4.57E-09 mr1219_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
vg0203428380 NA 2.17E-12 mr1219_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
vg0203428380 NA 5.61E-14 mr1274_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
vg0203428380 NA 5.83E-14 mr1274_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