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Detailed information for vg0717843035:

Variant ID: vg0717843035 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 17843035
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


AAACACCTCAAGACATTTGGCTGAATTTTGGGTATCGCAATATTCTTTTACATTTATGTTTCTTTCAGAATTTTAAATTCCAGAACTCTTAATTTACAGG[T/G]
TTTTTTTTTGTTGGTTTGTGTTCCGGGGAAGATGATTGAGCCTGAACTTGCCTTTGCGGATCTAAATGATGACATGGCATGTGCGAGTTCATATCTCCAG

Reverse complement sequence

CTGGAGATATGAACTCGCACATGCCATGTCATCATTTAGATCCGCAAAGGCAAGTTCAGGCTCAATCATCTTCCCCGGAACACAAACCAACAAAAAAAAA[A/C]
CCTGTAAATTAAGAGTTCTGGAATTTAAAATTCTGAAAGAAACATAAATGTAAAAGAATATTGCGATACCCAAAATTCAGCCAAATGTCTTGAGGTGTTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.50% 1.10% 0.40% 0.00% NA
All Indica  2759 97.50% 1.80% 0.69% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.00% 0.50% 0.50% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.20% 0.50% 0.22% 0.00% NA
Indica Intermediate  786 93.10% 5.10% 1.78% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0717843035 T -> G LOC_Os07g30190.1 downstream_gene_variant ; 4761.0bp to feature; MODIFIER silent_mutation Average:48.96; most accessible tissue: Callus, score: 84.332 N N N N
vg0717843035 T -> G LOC_Os07g30210.1 downstream_gene_variant ; 2109.0bp to feature; MODIFIER silent_mutation Average:48.96; most accessible tissue: Callus, score: 84.332 N N N N
vg0717843035 T -> G LOC_Os07g30210.2 downstream_gene_variant ; 2790.0bp to feature; MODIFIER silent_mutation Average:48.96; most accessible tissue: Callus, score: 84.332 N N N N
vg0717843035 T -> G LOC_Os07g30200.1 intron_variant ; MODIFIER silent_mutation Average:48.96; most accessible tissue: Callus, score: 84.332 N N N N
vg0717843035 T -> G LOC_Os07g30200.2 intron_variant ; MODIFIER silent_mutation Average:48.96; most accessible tissue: Callus, score: 84.332 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0717843035 NA 7.38E-07 mr1096 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
vg0717843035 NA 3.13E-07 mr1244_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
vg0717843035 3.18E-06 2.81E-07 mr1265_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
vg0717843035 7.28E-09 8.13E-11 mr1528_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