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Detailed information for vg1004522984:

Variant ID: vg1004522984 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4522984
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAGGGAGAAAAAAAGAAAATAATAATAATAATGTGCGATGTCGTCGTCTACATGGCATGCCACATAGGCAAGACCACGGTCAAATGAGACTTTGGACC[G/A]
GAAAGACATAATAAACCAAGTTTAGGGACCTCGATACATACACTAAAGATGATCTTTAGTCCCGGTTAAAAAGGGTAACGGGCATATTTGATCTTTAGTC

Reverse complement sequence

GACTAAAGATCAAATATGCCCGTTACCCTTTTTAACCGGGACTAAAGATCATCTTTAGTGTATGTATCGAGGTCCCTAAACTTGGTTTATTATGTCTTTC[C/T]
GGTCCAAAGTCTCATTTGACCGTGGTCTTGCCTATGTGGCATGCCATGTAGACGACGACATCGCACATTATTATTATTATTTTCTTTTTTTCTCCCTTCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.90% 16.60% 0.08% 2.43% NA
All Indica  2759 84.40% 15.30% 0.04% 0.29% NA
All Japonica  1512 88.00% 5.00% 0.20% 6.88% NA
Aus  269 5.20% 94.80% 0.00% 0.00% NA
Indica I  595 59.50% 40.30% 0.17% 0.00% NA
Indica II  465 89.90% 10.10% 0.00% 0.00% NA
Indica III  913 95.70% 3.40% 0.00% 0.88% NA
Indica Intermediate  786 86.90% 13.10% 0.00% 0.00% NA
Temperate Japonica  767 96.70% 3.00% 0.26% 0.00% NA
Tropical Japonica  504 76.20% 3.60% 0.00% 20.24% NA
Japonica Intermediate  241 84.60% 14.10% 0.41% 0.83% NA
VI/Aromatic  96 80.20% 19.80% 0.00% 0.00% NA
Intermediate  90 78.90% 17.80% 0.00% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004522984 G -> A LOC_Os10g08350.1 upstream_gene_variant ; 1029.0bp to feature; MODIFIER silent_mutation Average:44.68; most accessible tissue: Zhenshan97 young leaf, score: 59.612 N N N N
vg1004522984 G -> A LOC_Os10g08340-LOC_Os10g08350 intergenic_region ; MODIFIER silent_mutation Average:44.68; most accessible tissue: Zhenshan97 young leaf, score: 59.612 N N N N
vg1004522984 G -> DEL N N silent_mutation Average:44.68; most accessible tissue: Zhenshan97 young leaf, score: 59.612 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004522984 NA 7.51E-07 mr1140 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
vg1004522984 NA 7.24E-06 mr1203 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
vg1004522984 NA 2.88E-07 mr1395 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
vg1004522984 NA 1.62E-07 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
vg1004522984 NA 6.46E-06 mr1618 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
vg1004522984 2.30E-06 6.29E-09 mr1913 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
vg1004522984 NA 1.29E-06 mr1071_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
vg1004522984 6.94E-08 NA mr1100_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
vg1004522984 2.71E-07 2.49E-09 mr1100_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
vg1004522984 NA 3.77E-07 mr1203_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
vg1004522984 NA 6.26E-08 mr1613_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
vg1004522984 NA 1.51E-06 mr1913_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