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Detailed information for vg0424199959:

Variant ID: vg0424199959 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24199959
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAAACAGCGTCCAATTGATGCCACAGTTTGGATGAATGCGGTGGACATCCACCAACGTCAAATTCCTCATAAAAGGAGCCAAATGTTTTGGGGTCTCC[A/G]
GTTGAATCCATACCTGCATAAGATAGAAGGAAACCAAGGACGAAGTGACGAACAATGAATACACATTCAAGTGATGTTTCCTTCAATGGTTCGCTACCGA

Reverse complement sequence

TCGGTAGCGAACCATTGAAGGAAACATCACTTGAATGTGTATTCATTGTTCGTCACTTCGTCCTTGGTTTCCTTCTATCTTATGCAGGTATGGATTCAAC[T/C]
GGAGACCCCAAAACATTTGGCTCCTTTTATGAGGAATTTGACGTTGGTGGATGTCCACCGCATTCATCCAAACTGTGGCATCAATTGGACGCTGTTTCTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 57.30% 40.70% 0.47% 1.57% NA
All Indica  2759 32.00% 65.70% 0.72% 1.59% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 58.70% 30.50% 0.00% 10.78% NA
Indica I  595 4.90% 93.90% 0.67% 0.50% NA
Indica II  465 84.30% 15.30% 0.43% 0.00% NA
Indica III  913 20.40% 74.90% 1.10% 3.61% NA
Indica Intermediate  786 35.10% 63.40% 0.51% 1.02% 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 70.00% 26.70% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0424199959 A -> DEL LOC_Os04g40780.1 N frameshift_variant Average:46.759; most accessible tissue: Callus, score: 86.818 N N N N
vg0424199959 A -> G LOC_Os04g40780.1 missense_variant ; p.Leu261Pro; MODERATE nonsynonymous_codon ; L261P Average:46.759; most accessible tissue: Callus, score: 86.818 probably damaging -2.029 TOLERATED 0.85

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424199959 NA 1.33E-13 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
vg0424199959 NA 4.61E-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
vg0424199959 NA 2.14E-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
vg0424199959 NA 1.71E-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
vg0424199959 NA 5.91E-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
vg0424199959 NA 1.91E-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
vg0424199959 NA 3.62E-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
vg0424199959 NA 1.29E-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
vg0424199959 NA 8.89E-07 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
vg0424199959 NA 6.29E-07 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
vg0424199959 NA 2.27E-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
vg0424199959 NA 9.02E-13 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
vg0424199959 NA 2.85E-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
vg0424199959 NA 3.28E-10 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
vg0424199959 NA 8.08E-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
vg0424199959 NA 4.11E-09 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
vg0424199959 NA 1.80E-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
vg0424199959 NA 2.96E-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
vg0424199959 NA 5.08E-17 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
vg0424199959 NA 5.06E-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
vg0424199959 NA 6.47E-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
vg0424199959 NA 7.78E-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