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Detailed information for vg0716110434:

Variant ID: vg0716110434 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 16110434
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.59, G: 0.41, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CCGACCCATGGTTCGGTCGAACCCTCCTCAGCGCCGCTCGATCCAGGGTTGGTGATGGATGGTGTGGATGGCTTCCCTATAGCGATTGAAGGGTATTACC[A/G]
ACCTTTCCAACCGCCATAACCATCACTACCTGTCTGTAAAAGGCTCACTCTCTCTCCATTTCAAGACACACCTCAAACAAGAAGATCATTTCATCTCTCA

Reverse complement sequence

TGAGAGATGAAATGATCTTCTTGTTTGAGGTGTGTCTTGAAATGGAGAGAGAGTGAGCCTTTTACAGACAGGTAGTGATGGTTATGGCGGTTGGAAAGGT[T/C]
GGTAATACCCTTCAATCGCTATAGGGAAGCCATCCACACCATCCATCACCAACCCTGGATCGAGCGGCGCTGAGGAGGGTTCGACCGAACCATGGGTCGG

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 51.50% 48.40% 0.08% 0.00% NA
All Indica  2759 27.50% 72.40% 0.07% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 8.20% 91.80% 0.00% 0.00% NA
Indica I  595 2.20% 97.60% 0.17% 0.00% NA
Indica II  465 72.30% 27.50% 0.22% 0.00% NA
Indica III  913 16.40% 83.60% 0.00% 0.00% NA
Indica Intermediate  786 33.20% 66.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 63.30% 34.40% 2.22% 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
vg0716110434 A -> G LOC_Os07g27570.1 upstream_gene_variant ; 3051.0bp to feature; MODIFIER silent_mutation Average:52.382; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N
vg0716110434 A -> G LOC_Os07g27590.1 upstream_gene_variant ; 1394.0bp to feature; MODIFIER silent_mutation Average:52.382; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N
vg0716110434 A -> G LOC_Os07g27580.1 downstream_gene_variant ; 1003.0bp to feature; MODIFIER silent_mutation Average:52.382; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N
vg0716110434 A -> G LOC_Os07g27580-LOC_Os07g27590 intergenic_region ; MODIFIER silent_mutation Average:52.382; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0716110434 NA 1.07E-12 mr1069 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
vg0716110434 NA 1.55E-06 mr1074 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
vg0716110434 NA 8.00E-19 mr1077 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
vg0716110434 NA 7.01E-06 mr1124 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
vg0716110434 NA 1.16E-27 mr1130 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
vg0716110434 NA 2.95E-07 mr1130 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
vg0716110434 NA 1.17E-13 mr1149 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
vg0716110434 NA 6.47E-17 mr1441 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
vg0716110434 NA 1.43E-06 mr1441 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
vg0716110434 NA 2.24E-07 mr1557 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
vg0716110434 NA 6.15E-07 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
vg0716110434 NA 5.58E-06 mr1918 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
vg0716110434 NA 5.49E-06 mr1942 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
vg0716110434 NA 1.35E-07 mr1072_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
vg0716110434 NA 2.78E-38 mr1075_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
vg0716110434 NA 1.82E-08 mr1075_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
vg0716110434 NA 3.00E-28 mr1077_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
vg0716110434 NA 1.02E-08 mr1077_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
vg0716110434 NA 3.26E-29 mr1149_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
vg0716110434 NA 5.36E-07 mr1149_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
vg0716110434 NA 7.30E-09 mr1222_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
vg0716110434 NA 1.77E-31 mr1441_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
vg0716110434 NA 3.80E-08 mr1441_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
vg0716110434 NA 2.76E-17 mr1592_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
vg0716110434 NA 6.39E-10 mr1598_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
vg0716110434 NA 1.53E-08 mr1861_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