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Detailed information for vg0137745220:

Variant ID: vg0137745220 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 37745220
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AACGAGGTGGTATCAACATATGATTGATTGAGTTTTAATTATTATAAATTAAAAAAAGATTAATATGATATTTTAGAGCAACTTTTATATATAAATGGCT[T/G]
GTTTACTTTGCTACCATTTTCAACCTTATATTTATTTGGCAAAGTTACCAATAAAGTGACTACATTTAATTTGTTGTTAAATTTTAGTAAGTACATATGA

Reverse complement sequence

TCATATGTACTTACTAAAATTTAACAACAAATTAAATGTAGTCACTTTATTGGTAACTTTGCCAAATAAATATAAGGTTGAAAATGGTAGCAAAGTAAAC[A/C]
AGCCATTTATATATAAAAGTTGCTCTAAAATATCATATTAATCTTTTTTTAATTTATAATAATTAAAACTCAATCAATCATATGTTGATACCACCTCGTT

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 92.80% 5.60% 0.11% 1.44% NA
All Indica  2759 88.00% 9.50% 0.18% 2.39% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.60% 0.00% 0.00% 7.39% NA
Indica II  465 87.70% 11.80% 0.43% 0.00% NA
Indica III  913 82.70% 16.60% 0.11% 0.55% NA
Indica Intermediate  786 90.70% 6.90% 0.25% 2.16% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 93.30% 4.40% 0.00% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0137745220 T -> G LOC_Os01g65010.1 upstream_gene_variant ; 2499.0bp to feature; MODIFIER silent_mutation Average:35.239; most accessible tissue: Callus, score: 65.212 N N N N
vg0137745220 T -> G LOC_Os01g65030.1 downstream_gene_variant ; 306.0bp to feature; MODIFIER silent_mutation Average:35.239; most accessible tissue: Callus, score: 65.212 N N N N
vg0137745220 T -> G LOC_Os01g65010-LOC_Os01g65030 intergenic_region ; MODIFIER silent_mutation Average:35.239; most accessible tissue: Callus, score: 65.212 N N N N
vg0137745220 T -> DEL N N silent_mutation Average:35.239; most accessible tissue: Callus, score: 65.212 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0137745220 NA 6.76E-06 mr1375 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
vg0137745220 2.43E-08 3.14E-09 mr1517_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
vg0137745220 NA 5.66E-08 mr1538_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