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Detailed information for vg0719534510:

Variant ID: vg0719534510 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19534510
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, A: 0.08, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


CGAACTCAAAAGTTCTTCGTCTCGTTGATTGGATAAAACTCCAACTACATGTAATAATAATCTACGTAAAAGAGATGCAAAGTCTAATAATAGTAAACCG[T/A]
ACTATTCAAGTGTAATATTCGGAGTACAGTTTGGGCATTGTCCATGCTAAAGTATTCAATTTGAGGTAGCTTGCATTGCAGTACTGCGTACAATCTGAAT

Reverse complement sequence

ATTCAGATTGTACGCAGTACTGCAATGCAAGCTACCTCAAATTGAATACTTTAGCATGGACAATGCCCAAACTGTACTCCGAATATTACACTTGAATAGT[A/T]
CGGTTTACTATTATTAGACTTTGCATCTCTTTTACGTAGATTATTATTACATGTAGTTGGAGTTTTATCCAATCAACGAGACGAAGAACTTTTGAGTTCG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.60% 43.40% 0.02% 0.00% NA
All Indica  2759 80.50% 19.50% 0.00% 0.00% NA
All Japonica  1512 19.30% 80.60% 0.07% 0.00% NA
Aus  269 8.60% 91.40% 0.00% 0.00% NA
Indica I  595 91.90% 8.10% 0.00% 0.00% NA
Indica II  465 68.60% 31.40% 0.00% 0.00% NA
Indica III  913 80.70% 19.30% 0.00% 0.00% NA
Indica Intermediate  786 78.80% 21.20% 0.00% 0.00% NA
Temperate Japonica  767 1.80% 98.20% 0.00% 0.00% NA
Tropical Japonica  504 52.20% 47.80% 0.00% 0.00% NA
Japonica Intermediate  241 6.20% 93.40% 0.41% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 53.30% 46.70% 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
vg0719534510 T -> A LOC_Os07g32710.1 3_prime_UTR_variant ; 264.0bp to feature; MODIFIER silent_mutation Average:71.081; most accessible tissue: Callus, score: 79.965 N N N N
vg0719534510 T -> A LOC_Os07g32700.1 downstream_gene_variant ; 4148.0bp to feature; MODIFIER silent_mutation Average:71.081; most accessible tissue: Callus, score: 79.965 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719534510 6.85E-07 7.40E-08 mr1088 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
vg0719534510 3.55E-06 NA mr1103 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
vg0719534510 NA 3.61E-33 mr1129 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
vg0719534510 7.46E-06 5.55E-06 mr1225 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
vg0719534510 NA 1.02E-06 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
vg0719534510 NA 1.44E-11 mr1540 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
vg0719534510 NA 4.58E-14 mr1927 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
vg0719534510 4.01E-06 NA mr1088_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
vg0719534510 2.54E-06 NA mr1088_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
vg0719534510 NA 4.44E-07 mr1220_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
vg0719534510 NA 4.63E-08 mr1364_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
vg0719534510 NA 2.90E-23 mr1422_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
vg0719534510 NA 5.13E-14 mr1583_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
vg0719534510 9.94E-06 NA mr1620_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
vg0719534510 NA 3.73E-14 mr1807_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