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Detailed information for vg0424199782:

Variant ID: vg0424199782 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24199782
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.02, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


ACATATCATTATTTCCTTTTTAAACTAAGCGTTTGAGAGTTATTGATGCTAAAAATTTTAGAAGTTTATGAATTATGGTTAGAGTGTGTATTACTGTTGT[G/A]
TTGTCTAGTAAGTGAGAACGAAGAACGAAGGCAGTACCGAAATACTAAGTATCTTCAAAAGAGGTGCTGCTTCCAAAAGAAACAGCGTCCAATTGATGCC

Reverse complement sequence

GGCATCAATTGGACGCTGTTTCTTTTGGAAGCAGCACCTCTTTTGAAGATACTTAGTATTTCGGTACTGCCTTCGTTCTTCGTTCTCACTTACTAGACAA[C/T]
ACAACAGTAATACACACTCTAACCATAATTCATAAACTTCTAAAATTTTTAGCATCAATAACTCTCAAACGCTTAGTTTAAAAAGGAAATAATGATATGT

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 57.20% 40.70% 0.21% 1.95% NA
All Indica  2759 31.90% 65.70% 0.25% 2.21% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 58.70% 30.50% 1.12% 9.67% NA
Indica I  595 4.70% 93.60% 0.17% 1.51% NA
Indica II  465 84.10% 15.30% 0.00% 0.65% NA
Indica III  913 20.30% 75.10% 0.55% 4.05% NA
Indica Intermediate  786 35.00% 63.40% 0.13% 1.53% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 67.80% 26.70% 0.00% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0424199782 G -> DEL N N silent_mutation Average:38.038; most accessible tissue: Callus, score: 79.457 N N N N
vg0424199782 G -> A LOC_Os04g40770.1 downstream_gene_variant ; 4432.0bp to feature; MODIFIER silent_mutation Average:38.038; most accessible tissue: Callus, score: 79.457 N N N N
vg0424199782 G -> A LOC_Os04g40790.1 downstream_gene_variant ; 2531.0bp to feature; MODIFIER silent_mutation Average:38.038; most accessible tissue: Callus, score: 79.457 N N N N
vg0424199782 G -> A LOC_Os04g40780.1 intron_variant ; MODIFIER silent_mutation Average:38.038; most accessible tissue: Callus, score: 79.457 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424199782 NA 8.51E-15 Grain_length Ind_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0424199782 NA 8.32E-10 mr1050 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
vg0424199782 NA 2.87E-07 mr1050 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
vg0424199782 NA 1.57E-06 mr1170 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
vg0424199782 NA 5.39E-11 mr1272 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
vg0424199782 NA 5.41E-09 mr1399 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
vg0424199782 NA 3.43E-07 mr1458 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
vg0424199782 NA 6.92E-07 mr1593 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
vg0424199782 NA 4.54E-06 mr1598 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
vg0424199782 NA 3.92E-06 mr1608 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
vg0424199782 NA 9.85E-06 mr1731 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
vg0424199782 NA 2.57E-06 mr1835 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
vg0424199782 NA 3.13E-08 mr1860 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
vg0424199782 NA 2.19E-12 mr1904 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
vg0424199782 NA 3.59E-06 mr1904 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
vg0424199782 NA 6.26E-11 mr1050_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
vg0424199782 NA 7.38E-07 mr1272_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
vg0424199782 NA 2.64E-08 mr1593_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
vg0424199782 NA 3.82E-10 mr1835_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
vg0424199782 NA 4.96E-07 mr1895_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
vg0424199782 NA 1.03E-16 mr1904_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
vg0424199782 NA 5.56E-08 mr1904_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
vg0424199782 NA 6.09E-06 mr1931_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
vg0424199782 NA 3.53E-06 mr1942_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