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Detailed information for vg0307384335:

Variant ID: vg0307384335 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 7384335
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGCATTTATGGTATACATATATATTTGGCTAATCGGTGGTTTAGTCTATCAAATGGTTATGGAAGGATTATGGCTATATATGCATCTATCTAAATAGCAC[G/A]
GTTACATACCAGAGGTTCTCTTGTTAGATGGATTTAGGATCAATCAAATAATGAATCATTTGTATTATTATTTAATTGATGGAGGCTTTACTTTAATTAT

Reverse complement sequence

ATAATTAAAGTAAAGCCTCCATCAATTAAATAATAATACAAATGATTCATTATTTGATTGATCCTAAATCCATCTAACAAGAGAACCTCTGGTATGTAAC[C/T]
GTGCTATTTAGATAGATGCATATATAGCCATAATCCTTCCATAACCATTTGATAGACTAAACCACCGATTAGCCAAATATATATGTATACCATAAATGCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.30% 2.70% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.90% 8.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 84.40% 15.60% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 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
vg0307384335 G -> A LOC_Os03g13640.1 downstream_gene_variant ; 2872.0bp to feature; MODIFIER silent_mutation Average:26.207; most accessible tissue: Minghui63 root, score: 40.262 N N N N
vg0307384335 G -> A LOC_Os03g13660.1 downstream_gene_variant ; 4938.0bp to feature; MODIFIER silent_mutation Average:26.207; most accessible tissue: Minghui63 root, score: 40.262 N N N N
vg0307384335 G -> A LOC_Os03g13640-LOC_Os03g13660 intergenic_region ; MODIFIER silent_mutation Average:26.207; most accessible tissue: Minghui63 root, score: 40.262 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0307384335 1.53E-06 8.42E-08 mr1171 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
vg0307384335 NA 1.86E-06 mr1210 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
vg0307384335 NA 1.49E-06 mr1305 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
vg0307384335 8.74E-06 2.15E-07 mr1358 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
vg0307384335 NA 1.55E-07 mr1585 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
vg0307384335 NA 3.94E-06 mr1586 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
vg0307384335 NA 3.48E-09 mr1712 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
vg0307384335 NA 1.45E-07 mr1946 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
vg0307384335 NA 9.23E-07 mr1977 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
vg0307384335 NA 6.53E-06 mr1305_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
vg0307384335 NA 1.19E-06 mr1585_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