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Detailed information for vg0407825943:

Variant ID: vg0407825943 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 7825943
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


AGATGTACCAGGATTTGAAAGAGGCGTATTGGTGGCCCAACATGAAAAGGGATGTAGCCGAATACGTAGCGCTATGCGACGTATGCCAGAGGGTGAAGGC[C/T]
GAGCATCAGCGGCCAGCGGGATCGTTGCAACCACTCAAAATTCCGGAATGGAAGTAGGATGAAATAGGCATGGATTTTATCGTCGGATTGCCCAAGACCG

Reverse complement sequence

CGGTCTTGGGCAATCCGACGATAAAATCCATGCCTATTTCATCCTACTTCCATTCCGGAATTTTGAGTGGTTGCAACGATCCCGCTGGCCGCTGATGCTC[G/A]
GCCTTCACCCTCTGGCATACGTCGCATAGCGCTACGTATTCGGCTACATCCCTTTTCATGTTGGGCCACCAATACGCCTCTTTCAAATCCTGGTACATCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 64.60% 20.60% 0.87% 13.94% NA
All Indica  2759 40.80% 34.90% 1.45% 22.87% NA
All Japonica  1512 99.70% 0.10% 0.00% 0.20% NA
Aus  269 99.30% 0.00% 0.00% 0.74% NA
Indica I  595 10.80% 83.20% 1.01% 5.04% NA
Indica II  465 53.30% 17.00% 1.29% 28.39% NA
Indica III  913 51.80% 15.20% 1.64% 31.33% NA
Indica Intermediate  786 43.30% 31.80% 1.65% 23.28% NA
Temperate Japonica  767 99.70% 0.10% 0.00% 0.13% NA
Tropical Japonica  504 99.60% 0.00% 0.00% 0.40% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 0.00% 0.00% 11.46% NA
Intermediate  90 77.80% 7.80% 1.11% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0407825943 C -> DEL N N silent_mutation Average:53.564; most accessible tissue: Zhenshan97 young leaf, score: 82.077 N N N N
vg0407825943 C -> T LOC_Os04g14010.1 upstream_gene_variant ; 70.0bp to feature; MODIFIER silent_mutation Average:53.564; most accessible tissue: Zhenshan97 young leaf, score: 82.077 N N N N
vg0407825943 C -> T LOC_Os04g14000.1 downstream_gene_variant ; 747.0bp to feature; MODIFIER silent_mutation Average:53.564; most accessible tissue: Zhenshan97 young leaf, score: 82.077 N N N N
vg0407825943 C -> T LOC_Os04g14020.1 downstream_gene_variant ; 1943.0bp to feature; MODIFIER silent_mutation Average:53.564; most accessible tissue: Zhenshan97 young leaf, score: 82.077 N N N N
vg0407825943 C -> T LOC_Os04g14000-LOC_Os04g14010 intergenic_region ; MODIFIER silent_mutation Average:53.564; most accessible tissue: Zhenshan97 young leaf, score: 82.077 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0407825943 1.75E-06 1.01E-43 mr1026 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
vg0407825943 NA 3.62E-20 mr1026 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
vg0407825943 NA 1.32E-06 mr1113 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
vg0407825943 NA 1.38E-06 mr1114 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
vg0407825943 NA 1.64E-06 mr1116 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
vg0407825943 NA 1.61E-17 mr1118 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
vg0407825943 1.69E-07 2.15E-20 mr1118 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
vg0407825943 2.72E-06 1.86E-41 mr1161 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
vg0407825943 NA 5.55E-19 mr1161 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
vg0407825943 9.96E-06 7.86E-24 mr1495 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
vg0407825943 2.59E-07 1.01E-24 mr1495 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
vg0407825943 NA 2.53E-08 mr1496 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
vg0407825943 NA 1.23E-10 mr1794 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
vg0407825943 NA 3.88E-06 mr1113_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
vg0407825943 NA 1.26E-06 mr1114_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
vg0407825943 NA 6.36E-22 mr1118_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
vg0407825943 1.38E-06 3.00E-27 mr1118_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
vg0407825943 NA 3.06E-09 mr1120_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
vg0407825943 NA 2.17E-06 mr1123_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
vg0407825943 6.65E-10 4.74E-47 mr1161_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
vg0407825943 2.63E-07 8.88E-24 mr1161_2 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
vg0407825943 NA 2.41E-08 mr1212_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
vg0407825943 NA 4.57E-07 mr1247_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
vg0407825943 NA 6.12E-31 mr1495_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
vg0407825943 1.48E-06 2.45E-28 mr1495_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
vg0407825943 NA 3.60E-09 mr1496_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
vg0407825943 NA 1.41E-20 mr1531_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
vg0407825943 NA 1.38E-08 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
vg0407825943 NA 4.26E-14 mr1794_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
vg0407825943 NA 2.00E-09 mr1936_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
vg0407825943 NA 6.89E-07 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