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Detailed information for vg0822783342:

Variant ID: vg0822783342 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 22783342
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.19, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:


AACCGGTCTTTCCGCCACCTCGGTACGTGTTCGACATGTTGCGTATATTTGATCTGTTCATGTTTTACTGCTTAGTTTACATGTGTAGATCTAATGATGT[G/A]
TTAATGCTAGTATACATCTGTAATGTCATGATTTATTTATGAAATATATTAAATCATTATATGCCTATATTCTCAACAATCCAAAAACTTTATTATAGGC

Reverse complement sequence

GCCTATAATAAAGTTTTTGGATTGTTGAGAATATAGGCATATAATGATTTAATATATTTCATAAATAAATCATGACATTACAGATGTATACTAGCATTAA[C/T]
ACATCATTAGATCTACACATGTAAACTAAGCAGTAAAACATGAACAGATCAAATATACGCAACATGTCGAACACGTACCGAGGTGGCGGAAAGACCGGTT

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 66.40% 33.50% 0.08% 0.00% NA
All Indica  2759 98.30% 1.70% 0.07% 0.00% NA
All Japonica  1512 1.60% 98.40% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 98.70% 1.20% 0.11% 0.00% NA
Indica Intermediate  786 97.20% 2.70% 0.13% 0.00% NA
Temperate Japonica  767 1.80% 98.20% 0.00% 0.00% NA
Tropical Japonica  504 0.80% 99.20% 0.00% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 4.20% 1.04% 0.00% NA
Intermediate  90 55.60% 43.30% 1.11% 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
vg0822783342 G -> A LOC_Os08g36150.1 upstream_gene_variant ; 2076.0bp to feature; MODIFIER silent_mutation Average:37.57; most accessible tissue: Zhenshan97 flag leaf, score: 61.926 N N N N
vg0822783342 G -> A LOC_Os08g36160.1 upstream_gene_variant ; 115.0bp to feature; MODIFIER silent_mutation Average:37.57; most accessible tissue: Zhenshan97 flag leaf, score: 61.926 N N N N
vg0822783342 G -> A LOC_Os08g36150.2 upstream_gene_variant ; 2182.0bp to feature; MODIFIER silent_mutation Average:37.57; most accessible tissue: Zhenshan97 flag leaf, score: 61.926 N N N N
vg0822783342 G -> A LOC_Os08g36150-LOC_Os08g36160 intergenic_region ; MODIFIER silent_mutation Average:37.57; most accessible tissue: Zhenshan97 flag leaf, score: 61.926 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0822783342 NA 3.95E-36 mr1542 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
vg0822783342 NA 5.03E-07 mr1915 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
vg0822783342 NA 8.96E-21 mr1276_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
vg0822783342 NA 1.59E-08 mr1322_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
vg0822783342 NA 9.92E-13 mr1325_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
vg0822783342 NA 4.44E-14 mr1326_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
vg0822783342 NA 3.23E-08 mr1335_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
vg0822783342 NA 7.06E-07 mr1418_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
vg0822783342 NA 2.19E-06 mr1488_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
vg0822783342 NA 1.06E-10 mr1506_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
vg0822783342 NA 3.45E-12 mr1553_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
vg0822783342 NA 1.05E-07 mr1683_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
vg0822783342 NA 1.61E-58 mr1695_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
vg0822783342 NA 5.42E-14 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
vg0822783342 NA 3.18E-06 mr1992_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