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Detailed information for vg0726950185:

Variant ID: vg0726950185 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 26950185
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, T: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


GTGACTTCCTTGTCGTCGTCATTGGCATCCCTCTGTTCCTGCATTTCGCTCCTTCGGTCTTCCTCTTGCCCTAGTAATTGCAGGTTGAAGCTTGGTCTCG[G/T]
AAGCACAATCTTCTCCATGGACTGATTATTGTTCTTCGGTTCGTTTCCATCTCCAATCAGTGGCAGCATAGTAGGTTTTGTTGTGTTGAACAACCTGTGG

Reverse complement sequence

CCACAGGTTGTTCAACACAACAAAACCTACTATGCTGCCACTGATTGGAGATGGAAACGAACCGAAGAACAATAATCAGTCCATGGAGAAGATTGTGCTT[C/A]
CGAGACCAAGCTTCAACCTGCAATTACTAGGGCAAGAGGAAGACCGAAGGAGCGAAATGCAGGAACAGAGGGATGCCAATGACGACGACAAGGAAGTCAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.40% 1.80% 0.83% 0.00% NA
All Indica  2759 95.50% 3.00% 1.41% 0.00% 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 89.40% 6.40% 4.20% 0.00% NA
Indica II  465 95.30% 4.30% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 95.20% 3.30% 1.53% 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  90 100.00% 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
vg0726950185 G -> T LOC_Os07g45150.1 missense_variant ; p.Pro63Thr; MODERATE nonsynonymous_codon ; P63T Average:68.581; most accessible tissue: Callus, score: 87.881 unknown unknown TOLERATED 0.36

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0726950185 3.90E-07 1.25E-11 mr1038 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
vg0726950185 6.00E-10 3.83E-16 mr1389 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
vg0726950185 4.47E-13 1.71E-19 mr1038_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
vg0726950185 3.57E-07 NA mr1141_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
vg0726950185 NA 2.54E-06 mr1236_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
vg0726950185 6.49E-12 7.52E-17 mr1389_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