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Detailed information for vg0709453116:

Variant ID: vg0709453116 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9453116
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.07, others allele: 0.00, population size: 72. )

Flanking Sequence (100 bp) in Reference Genome:


GTGAATTATTTGTATTATTATTTTATTGATGGAAGCTTTACTTTAATTATGAACATATTTTACTTGCCATTATAAATTATAAAAGGGCTAATAATTATCC[C/A]
TGCTCTATATGTTACACTTGTGAGGCTAATAATATTATAGTTACAGATTATCTCATCACATAATTTTACAATGAATAATCTTAATTTACAATTGAACTTA

Reverse complement sequence

TAAGTTCAATTGTAAATTAAGATTATTCATTGTAAAATTATGTGATGAGATAATCTGTAACTATAATATTATTAGCCTCACAAGTGTAACATATAGAGCA[G/T]
GGATAATTATTAGCCCTTTTATAATTTATAATGGCAAGTAAAATATGTTCATAATTAAAGTAAAGCTTCCATCAATAAAATAATAATACAAATAATTCAC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.80% 1.00% 15.51% 50.74% NA
All Indica  2759 2.70% 1.60% 16.24% 79.52% NA
All Japonica  1512 83.20% 0.10% 9.33% 7.41% NA
Aus  269 61.70% 0.40% 24.54% 13.38% NA
Indica I  595 2.50% 1.00% 12.61% 83.87% NA
Indica II  465 3.90% 3.20% 13.98% 78.92% NA
Indica III  913 0.70% 1.60% 15.12% 82.58% NA
Indica Intermediate  786 4.50% 0.90% 21.63% 73.03% NA
Temperate Japonica  767 88.10% 0.00% 1.69% 10.17% NA
Tropical Japonica  504 83.50% 0.00% 14.88% 1.59% NA
Japonica Intermediate  241 66.80% 0.40% 21.99% 10.79% NA
VI/Aromatic  96 19.80% 1.00% 62.50% 16.67% NA
Intermediate  90 35.60% 0.00% 20.00% 44.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0709453116 C -> DEL N N silent_mutation Average:18.346; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 N N N N
vg0709453116 C -> A LOC_Os07g16210.1 upstream_gene_variant ; 1824.0bp to feature; MODIFIER silent_mutation Average:18.346; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 N N N N
vg0709453116 C -> A LOC_Os07g16190-LOC_Os07g16210 intergenic_region ; MODIFIER silent_mutation Average:18.346; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709453116 NA 1.91E-22 mr1051 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
vg0709453116 4.71E-06 NA mr1123 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
vg0709453116 NA 1.03E-16 mr1147 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
vg0709453116 NA 7.94E-10 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
vg0709453116 8.87E-06 NA mr1247 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
vg0709453116 NA 1.80E-06 mr1280 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
vg0709453116 NA 7.62E-10 mr1299 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
vg0709453116 NA 4.51E-10 mr1379 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
vg0709453116 NA 6.11E-23 mr1416 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
vg0709453116 NA 1.77E-07 mr1559 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
vg0709453116 NA 3.36E-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
vg0709453116 NA 8.67E-06 mr1652 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
vg0709453116 NA 9.62E-07 mr1756 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
vg0709453116 NA 4.06E-06 mr1788 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
vg0709453116 NA 1.29E-08 mr1804 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
vg0709453116 NA 7.87E-06 mr1875 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
vg0709453116 3.04E-07 NA mr1113_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
vg0709453116 2.73E-07 NA mr1114_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
vg0709453116 1.29E-06 NA mr1117_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
vg0709453116 2.38E-06 NA mr1119_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
vg0709453116 4.21E-08 NA mr1120_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
vg0709453116 1.65E-06 NA mr1123_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
vg0709453116 2.21E-06 NA mr1240_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
vg0709453116 1.20E-06 NA mr1242_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
vg0709453116 2.44E-07 NA mr1247_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
vg0709453116 9.61E-06 NA mr1496_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
vg0709453116 NA 1.87E-06 mr1559_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
vg0709453116 NA 5.44E-08 mr1690_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
vg0709453116 NA 7.72E-07 mr1788_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
vg0709453116 NA 3.75E-06 mr1872_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