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Detailed information for vg0711049866:

Variant ID: vg0711049866 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 11049866
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTCAGCGGGAGAGAGAGAGGAGAGCGGCGGCTTGGCTTGGTGGGCTAGCTGGGCCGGGCGCGCACAGGCCGGAGAGAGAGGGGTTTTGGGCCGACTTTCG[G/A]
CCCAAAGCCAAAAGAGGACTATTAAAACCTTTTTCTATTTAAATTATTCGTGAAATGCAATTCCATTTATTAAAAATACTTCCTTGGCTCAAATGAATCC

Reverse complement sequence

GGATTCATTTGAGCCAAGGAAGTATTTTTAATAAATGGAATTGCATTTCACGAATAATTTAAATAGAAAAAGGTTTTAATAGTCCTCTTTTGGCTTTGGG[C/T]
CGAAAGTCGGCCCAAAACCCCTCTCTCTCCGGCCTGTGCGCGCCCGGCCCAGCTAGCCCACCAAGCCAAGCCGCCGCTCTCCTCTCTCTCTCCCGCTGAC

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 63.50% 27.20% 0.34% 8.97% NA
All Indica  2759 96.70% 1.20% 0.29% 1.88% NA
All Japonica  1512 1.80% 79.10% 0.33% 18.78% NA
Aus  269 90.30% 4.80% 0.00% 4.83% NA
Indica I  595 99.00% 0.50% 0.50% 0.00% NA
Indica II  465 96.60% 3.20% 0.22% 0.00% NA
Indica III  913 99.70% 0.10% 0.11% 0.11% NA
Indica Intermediate  786 91.50% 1.70% 0.38% 6.49% NA
Temperate Japonica  767 1.70% 66.00% 0.52% 31.81% NA
Tropical Japonica  504 0.80% 98.80% 0.00% 0.40% NA
Japonica Intermediate  241 4.10% 79.70% 0.41% 15.77% NA
VI/Aromatic  96 16.70% 6.20% 3.12% 73.96% NA
Intermediate  90 53.30% 42.20% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0711049866 G -> DEL N N silent_mutation Average:51.608; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N
vg0711049866 G -> A LOC_Os07g18690.1 upstream_gene_variant ; 2064.0bp to feature; MODIFIER silent_mutation Average:51.608; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N
vg0711049866 G -> A LOC_Os07g18700.1 downstream_gene_variant ; 1071.0bp to feature; MODIFIER silent_mutation Average:51.608; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N
vg0711049866 G -> A LOC_Os07g18690-LOC_Os07g18700 intergenic_region ; MODIFIER silent_mutation Average:51.608; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0711049866 4.05E-06 1.09E-76 mr1100 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
vg0711049866 NA 9.75E-07 mr1100 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
vg0711049866 NA 3.60E-27 mr1238 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
vg0711049866 NA 1.17E-28 mr1309 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
vg0711049866 NA 8.25E-18 mr1484 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
vg0711049866 NA 1.54E-11 mr1609 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
vg0711049866 NA 7.36E-06 mr1613 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
vg0711049866 NA 2.99E-11 mr1626 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
vg0711049866 3.21E-06 3.21E-06 mr1855 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
vg0711049866 NA 2.40E-15 mr1900 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
vg0711049866 NA 1.84E-10 mr1905 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
vg0711049866 NA 6.22E-11 mr1945 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
vg0711049866 NA 7.91E-06 mr1962 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
vg0711049866 NA 6.76E-08 mr1004_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
vg0711049866 NA 4.58E-19 mr1062_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
vg0711049866 NA 1.13E-06 mr1062_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
vg0711049866 NA 3.03E-07 mr1167_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
vg0711049866 NA 1.09E-27 mr1238_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
vg0711049866 NA 4.15E-26 mr1484_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
vg0711049866 NA 4.10E-15 mr1726_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
vg0711049866 NA 5.15E-07 mr1726_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
vg0711049866 NA 1.64E-13 mr1838_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
vg0711049866 NA 1.55E-32 mr1841_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
vg0711049866 NA 7.38E-21 mr1900_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
vg0711049866 NA 2.74E-20 mr1945_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
vg0711049866 NA 6.56E-14 mr1950_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
vg0711049866 5.82E-07 5.82E-07 mr1950_2 Jap_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
vg0711049866 NA 9.19E-12 mr1986_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