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Detailed information for vg0726174758:

Variant ID: vg0726174758 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26174758
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


ACAGAGGCTCATTCAGATTTGTAGTATTAAAATATATCTAGATTCATAGGGTCTGTTTGGTACAGCTCCAACTCCTAAATTTAACTCCAGGAGTTGAGTC[T/C]
GGAGTGGAGTTGTGGAGCTGTCTAAACCCAGCTCCACAACTCTAGTTCATTTTGTGAGAGCTCCACTACCAGTTTTGGTGGAGCTGAAACTGTTTGGCTG

Reverse complement sequence

CAGCCAAACAGTTTCAGCTCCACCAAAACTGGTAGTGGAGCTCTCACAAAATGAACTAGAGTTGTGGAGCTGGGTTTAGACAGCTCCACAACTCCACTCC[A/G]
GACTCAACTCCTGGAGTTAAATTTAGGAGTTGGAGCTGTACCAAACAGACCCTATGAATCTAGATATATTTTAATACTACAAATCTGAATGAGCCTCTGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.90% 9.00% 0.11% 0.00% NA
All Indica  2759 86.70% 13.20% 0.18% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 78.40% 21.60% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 93.50% 6.50% 0.00% 0.00% NA
Indica III  913 76.90% 23.00% 0.11% 0.00% NA
Indica Intermediate  786 84.90% 14.60% 0.51% 0.00% 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 96.70% 3.30% 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
vg0726174758 T -> C LOC_Os07g43750.1 upstream_gene_variant ; 1820.0bp to feature; MODIFIER silent_mutation Average:65.939; most accessible tissue: Minghui63 root, score: 83.399 N N N N
vg0726174758 T -> C LOC_Os07g43730.1 downstream_gene_variant ; 2202.0bp to feature; MODIFIER silent_mutation Average:65.939; most accessible tissue: Minghui63 root, score: 83.399 N N N N
vg0726174758 T -> C LOC_Os07g43740.1 downstream_gene_variant ; 372.0bp to feature; MODIFIER silent_mutation Average:65.939; most accessible tissue: Minghui63 root, score: 83.399 N N N N
vg0726174758 T -> C LOC_Os07g43740-LOC_Os07g43750 intergenic_region ; MODIFIER silent_mutation Average:65.939; most accessible tissue: Minghui63 root, score: 83.399 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726174758 NA 8.42E-06 mr1107 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
vg0726174758 NA 4.11E-07 mr1226 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
vg0726174758 NA 1.88E-06 mr1144_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
vg0726174758 NA 5.85E-08 mr1155_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
vg0726174758 NA 4.60E-06 mr1168_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
vg0726174758 4.17E-06 NA mr1198_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
vg0726174758 NA 2.87E-06 mr1620_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