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Detailed information for vg0811120484:

Variant ID: vg0811120484 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 11120484
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAGTACAGGAGTATCCTGAGGTGTTTCCTGAAGACCTCACTACAATGCCACCAAAGAGAGAAATCGAGTTCCAGATTGACCTGGTTAAGGTAACCACTCC[G/A]
ATTTACAAGAGGCCATACAGAATTGCAGCTAATGAGCTAGCAGAGGTCAAGAAGCAAGTTGATGAACAGCTGTAGAAAGGGTACATCCGACCGAGTACTT

Reverse complement sequence

AAGTACTCGGTCGGATGTACCCTTTCTACAGCTGTTCATCAACTTGCTTCTTGACCTCTGCTAGCTCATTAGCTGCAATTCTGTATGGCCTCTTGTAAAT[C/T]
GGAGTGGTTACCTTAACCAGGTCAATCTGGAACTCGATTTCTCTCTTTGGTGGCATTGTAGTGAGGTCTTCAGGAAACACCTCAGGATACTCCTGTACTA

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 48.10% 31.10% 0.38% 20.40% NA
All Indica  2759 78.70% 12.40% 0.40% 8.45% NA
All Japonica  1512 2.50% 55.80% 0.46% 41.27% NA
Aus  269 7.80% 91.80% 0.00% 0.37% NA
Indica I  595 97.10% 0.80% 0.00% 2.02% NA
Indica II  465 87.10% 7.70% 0.22% 4.95% NA
Indica III  913 64.40% 20.30% 0.22% 15.12% NA
Indica Intermediate  786 76.50% 14.90% 1.02% 7.63% NA
Temperate Japonica  767 2.20% 87.90% 0.00% 9.91% NA
Tropical Japonica  504 2.20% 14.50% 1.39% 81.94% NA
Japonica Intermediate  241 4.10% 39.80% 0.00% 56.02% NA
VI/Aromatic  96 7.30% 5.20% 0.00% 87.50% NA
Intermediate  90 37.80% 37.80% 0.00% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0811120484 G -> A LOC_Os08g18130.1 downstream_gene_variant ; 3122.0bp to feature; MODIFIER silent_mutation Average:40.273; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 N N N N
vg0811120484 G -> A LOC_Os08g18140.1 intron_variant ; MODIFIER silent_mutation Average:40.273; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 N N N N
vg0811120484 G -> DEL N N silent_mutation Average:40.273; most accessible tissue: Zhenshan97 flag leaf, score: 56.01 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0811120484 NA 4.90E-07 mr1206 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
vg0811120484 NA 2.08E-06 mr1668 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
vg0811120484 NA 8.28E-06 mr1689 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
vg0811120484 5.79E-06 NA mr1089_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
vg0811120484 3.35E-06 NA mr1109_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
vg0811120484 NA 6.93E-06 mr1129_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
vg0811120484 NA 1.28E-12 mr1241_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
vg0811120484 6.76E-06 NA mr1402_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
vg0811120484 NA 3.80E-08 mr1404_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
vg0811120484 7.05E-06 NA mr1423_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
vg0811120484 9.19E-06 NA mr1599_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
vg0811120484 NA 3.49E-07 mr1671_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