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Detailed information for vg0431043984:

Variant ID: vg0431043984 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31043984
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )

Flanking Sequence (100 bp) in Reference Genome:


ACCAGTACTAGTGATTATCTCCATCACTCTCTCACTTCACTTGGAGAGATTAATTAGTTGGAGTGTGTGCTGTGCTATCAGTGTGTCTTTCTTTGTGTTT[C/A]
TTTTTGGTTTGGACGTTTTGCCTTTAATTTCTTGTTGTTTAATTTTGGTATCTATGCTTTCTTGCCACTAGAGCAAAACTGAGAGAGAGATAGAGGGATA

Reverse complement sequence

TATCCCTCTATCTCTCTCTCAGTTTTGCTCTAGTGGCAAGAAAGCATAGATACCAAAATTAAACAACAAGAAATTAAAGGCAAAACGTCCAAACCAAAAA[G/T]
AAACACAAAGAAAGACACACTGATAGCACAGCACACACTCCAACTAATTAATCTCTCCAAGTGAAGTGAGAGAGTGATGGAGATAATCACTAGTACTGGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.00% 3.80% 0.21% 0.00% NA
All Indica  2759 99.30% 0.60% 0.07% 0.00% NA
All Japonica  1512 88.80% 10.70% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.30% 1.30% 0.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 78.70% 20.20% 1.04% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 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  90 100.00% 0.00% 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
vg0431043984 C -> A LOC_Os04g52240.1 downstream_gene_variant ; 559.0bp to feature; MODIFIER silent_mutation Average:71.275; most accessible tissue: Callus, score: 94.088 N N N N
vg0431043984 C -> A LOC_Os04g52240-LOC_Os04g52250 intergenic_region ; MODIFIER silent_mutation Average:71.275; most accessible tissue: Callus, score: 94.088 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431043984 5.13E-07 NA mr1062_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
vg0431043984 NA 2.25E-09 mr1062_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
vg0431043984 7.23E-06 NA mr1186_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
vg0431043984 5.68E-06 5.68E-06 mr1360_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
vg0431043984 7.53E-07 NA mr1371_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
vg0431043984 NA 9.53E-07 mr1439_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
vg0431043984 9.57E-07 7.52E-07 mr1445_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
vg0431043984 4.52E-06 4.52E-06 mr1445_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
vg0431043984 2.32E-06 NA mr1648_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
vg0431043984 6.59E-07 NA mr1655_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
vg0431043984 4.54E-06 4.54E-06 mr1655_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
vg0431043984 9.66E-07 NA mr1669_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
vg0431043984 NA 1.83E-06 mr1765_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