\

Search for Variation information by Variation ID:

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

Detailed information for vg0507041473:

Variant ID: vg0507041473 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7041473
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:


ACAAAACCACACTATCAATAAATGGATTCACATGTGAGATGACGTAGTTGTTACACCTAGGATGAGAATATGGCATCCTATTAATTTCGTGTGATGGCTG[G/T]
TAATAAGATGCCACGTCCTCGTCATAAGTGGAACAGCCACGCCATATCACGGGTGAATCAATTCATTGATAGTGTGATTTTCTGAAACTACACTACTAAA

Reverse complement sequence

TTTAGTAGTGTAGTTTCAGAAAATCACACTATCAATGAATTGATTCACCCGTGATATGGCGTGGCTGTTCCACTTATGACGAGGACGTGGCATCTTATTA[C/A]
CAGCCATCACACGAAATTAATAGGATGCCATATTCTCATCCTAGGTGTAACAACTACGTCATCTCACATGTGAATCCATTTATTGATAGTGTGGTTTTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.70% 29.80% 0.15% 0.42% NA
All Indica  2759 51.20% 48.10% 0.22% 0.54% NA
All Japonica  1512 99.50% 0.30% 0.07% 0.13% NA
Aus  269 77.30% 22.70% 0.00% 0.00% NA
Indica I  595 28.20% 71.80% 0.00% 0.00% NA
Indica II  465 75.10% 24.30% 0.22% 0.43% NA
Indica III  913 56.20% 42.80% 0.11% 0.88% NA
Indica Intermediate  786 48.60% 50.30% 0.51% 0.64% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.60% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 0.40% 0.00% 0.83% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 80.00% 16.70% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0507041473 G -> T LOC_Os05g12260.1 downstream_gene_variant ; 4719.0bp to feature; MODIFIER silent_mutation Average:45.69; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0507041473 G -> T LOC_Os05g12270.1 downstream_gene_variant ; 1114.0bp to feature; MODIFIER silent_mutation Average:45.69; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0507041473 G -> T LOC_Os05g12270-LOC_Os05g12280 intergenic_region ; MODIFIER silent_mutation Average:45.69; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N
vg0507041473 G -> DEL N N silent_mutation Average:45.69; most accessible tissue: Zhenshan97 panicle, score: 61.671 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507041473 NA 5.24E-12 mr1195 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
vg0507041473 2.63E-10 1.11E-23 mr1531 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
vg0507041473 1.82E-10 1.75E-15 mr1531 Ind_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
vg0507041473 8.48E-21 1.17E-27 mr1593 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
vg0507041473 1.27E-16 2.22E-32 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
vg0507041473 NA 2.70E-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
vg0507041473 NA 5.72E-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
vg0507041473 4.17E-10 8.33E-27 mr1195_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
vg0507041473 1.85E-08 2.54E-14 mr1195_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
vg0507041473 NA 3.27E-09 mr1531_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
vg0507041473 1.24E-23 5.50E-35 mr1593_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
vg0507041473 1.48E-18 5.54E-44 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
vg0507041473 NA 8.46E-06 mr1961_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