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Detailed information for vg0726127290:

Variant ID: vg0726127290 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26127290
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.05, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTAAAAAGATATTTAAACCTCTCTTCTATTTTTTTTAAAAAATAATCCATTCTCAAGATGTCTAGTTTCTTTGGGTCTGTGTATTATATTTATTTGG[G/A]
TGATCCAAATAAGAAGATGATAATAATTCGTTTTTGATGCATGCGTCAGTGGTAGTCGTGTCTTGAGTACTTTGTAATGAAAATTTTGTTATCTCTCAAT

Reverse complement sequence

ATTGAGAGATAACAAAATTTTCATTACAAAGTACTCAAGACACGACTACCACTGACGCATGCATCAAAAACGAATTATTATCATCTTCTTATTTGGATCA[C/T]
CCAAATAAATATAATACACAGACCCAAAGAAACTAGACATCTTGAGAATGGATTATTTTTTAAAAAAAATAGAAGAGAGGTTTAAATATCTTTTTAAAAA

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 59.20% 40.60% 0.21% 0.00% NA
All Indica  2759 31.30% 68.40% 0.36% 0.00% NA
All Japonica  1512 99.10% 0.90% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 20.20% 79.50% 0.34% 0.00% NA
Indica II  465 15.10% 84.90% 0.00% 0.00% NA
Indica III  913 46.00% 53.80% 0.22% 0.00% NA
Indica Intermediate  786 32.20% 67.00% 0.76% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 81.10% 18.90% 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
vg0726127290 G -> A LOC_Os07g43640.1 intron_variant ; MODIFIER silent_mutation Average:31.472; most accessible tissue: Callus, score: 64.184 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726127290 NA 2.84E-06 mr1212 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
vg0726127290 NA 5.98E-33 mr1213 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
vg0726127290 NA 8.72E-08 mr1213 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
vg0726127290 NA 3.46E-08 mr1246 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
vg0726127290 NA 1.19E-06 mr1586 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
vg0726127290 NA 2.38E-09 mr1172_2 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
vg0726127290 2.54E-07 NA mr1246_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
vg0726127290 NA 4.39E-11 mr1246_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
vg0726127290 NA 1.26E-12 mr1409_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
vg0726127290 NA 1.03E-10 mr1649_2 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