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Detailed information for vg0918359050:

Variant ID: vg0918359050 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18359050
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.79, A: 0.21, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TGAATGATGAGGGGTATAAGTGTCATTTATGAAAAGAGTTGTTGGTTTAAGGATAAGTTTGAACTAAAATGAAAACTTGAAGGACTAATATGGATAGATT[A/G]
AAACATCAAGGACTAAACTGAGCTTCAGTGAAACTTGGAGAACCACTTTAGCTATTCACCCTAATATAAAAAAAAGGAGTAGATGGCAAGGTGTGTCTTG

Reverse complement sequence

CAAGACACACCTTGCCATCTACTCCTTTTTTTTATATTAGGGTGAATAGCTAAAGTGGTTCTCCAAGTTTCACTGAAGCTCAGTTTAGTCCTTGATGTTT[T/C]
AATCTATCCATATTAGTCCTTCAAGTTTTCATTTTAGTTCAAACTTATCCTTAAACCAACAACTCTTTTCATAAATGACACTTATACCCCTCATCATTCA

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 77.30% 22.50% 0.23% 0.00% NA
All Indica  2759 63.00% 36.60% 0.40% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 83.60% 16.40% 0.00% 0.00% NA
Indica I  595 53.80% 45.50% 0.67% 0.00% NA
Indica II  465 89.00% 11.00% 0.00% 0.00% NA
Indica III  913 50.10% 49.70% 0.22% 0.00% NA
Indica Intermediate  786 69.60% 29.80% 0.64% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 0.00% 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
vg0918359050 A -> G LOC_Os09g30170.1 upstream_gene_variant ; 1621.0bp to feature; MODIFIER silent_mutation Average:64.78; most accessible tissue: Minghui63 root, score: 81.681 N N N N
vg0918359050 A -> G LOC_Os09g30170.2 upstream_gene_variant ; 1621.0bp to feature; MODIFIER silent_mutation Average:64.78; most accessible tissue: Minghui63 root, score: 81.681 N N N N
vg0918359050 A -> G LOC_Os09g30170.3 upstream_gene_variant ; 1621.0bp to feature; MODIFIER silent_mutation Average:64.78; most accessible tissue: Minghui63 root, score: 81.681 N N N N
vg0918359050 A -> G LOC_Os09g30160-LOC_Os09g30170 intergenic_region ; MODIFIER silent_mutation Average:64.78; most accessible tissue: Minghui63 root, score: 81.681 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918359050 2.18E-06 NA mr1557 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
vg0918359050 NA 3.66E-06 mr1970 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
vg0918359050 NA 1.61E-06 mr1973 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
vg0918359050 7.04E-07 NA mr1557_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
vg0918359050 NA 4.27E-08 mr1557_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