Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0407576542:

Variant ID: vg0407576542 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7576542
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, T: 0.34, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


CAGATAGCGTCCGTTACAGATGACTACTAACCTCAATCGGGTACTAAGTTATGACCCGTCACAAATGAGTATAATCCACAAAAAATATTAATTTTGTTTT[A/T]
TGGCTAGCTTCAGGCCTTTGCTAGCCATACCCGCTGTAAAAATGACAGAAACACATGCATATACAATATCCCCAGCATCACCCATTCATATACATGCATT

Reverse complement sequence

AATGCATGTATATGAATGGGTGATGCTGGGGATATTGTATATGCATGTGTTTCTGTCATTTTTACAGCGGGTATGGCTAGCAAAGGCCTGAAGCTAGCCA[T/A]
AAAACAAAATTAATATTTTTTGTGGATTATACTCATTTGTGACGGGTCATAACTTAGTACCCGATTGAGGTTAGTAGTCATCTGTAACGGACGCTATCTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 22.00% 13.80% 0.32% 63.86% NA
All Indica  2759 1.80% 2.00% 0.43% 95.69% NA
All Japonica  1512 63.30% 35.20% 0.00% 1.52% NA
Aus  269 0.40% 0.00% 0.37% 99.26% NA
Indica I  595 2.20% 0.20% 0.17% 97.48% NA
Indica II  465 2.20% 2.60% 0.86% 94.41% NA
Indica III  913 1.00% 3.00% 0.55% 95.51% NA
Indica Intermediate  786 2.40% 2.00% 0.25% 95.29% NA
Temperate Japonica  767 96.00% 3.50% 0.00% 0.52% NA
Tropical Japonica  504 9.90% 87.30% 0.00% 2.78% NA
Japonica Intermediate  241 71.00% 27.00% 0.00% 2.07% NA
VI/Aromatic  96 8.30% 42.70% 1.04% 47.92% NA
Intermediate  90 25.60% 26.70% 1.11% 46.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0407576542 A -> DEL N N silent_mutation Average:10.421; most accessible tissue: Callus, score: 54.711 N N N N
vg0407576542 A -> T LOC_Os04g13560.1 downstream_gene_variant ; 741.0bp to feature; MODIFIER silent_mutation Average:10.421; most accessible tissue: Callus, score: 54.711 N N N N
vg0407576542 A -> T LOC_Os04g13550-LOC_Os04g13560 intergenic_region ; MODIFIER silent_mutation Average:10.421; most accessible tissue: Callus, score: 54.711 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407576542 1.49E-08 NA mr1071 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
vg0407576542 3.21E-06 NA mr1080 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
vg0407576542 7.19E-08 NA mr1140 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
vg0407576542 1.55E-07 NA mr1203 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
vg0407576542 7.57E-06 2.78E-23 mr1301 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
vg0407576542 NA 3.12E-15 mr1301 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
vg0407576542 5.61E-07 NA mr1618 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
vg0407576542 NA 9.94E-09 mr1648 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
vg0407576542 NA 8.28E-07 mr1993 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
vg0407576542 NA 6.08E-08 mr1993 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
vg0407576542 1.72E-07 NA mr1071_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
vg0407576542 3.06E-09 NA mr1080_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
vg0407576542 3.79E-06 NA mr1100_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
vg0407576542 9.55E-10 NA mr1203_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
vg0407576542 NA 1.00E-22 mr1301_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
vg0407576542 NA 2.04E-18 mr1301_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
vg0407576542 NA 5.41E-06 mr1398_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
vg0407576542 8.01E-08 NA mr1613_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
vg0407576542 1.20E-07 NA mr1619_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
vg0407576542 NA 2.21E-11 mr1993_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
vg0407576542 NA 1.57E-12 mr1993_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