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Detailed information for vg1003086515:

Variant ID: vg1003086515 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 3086515
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


AGCACATTGACTAATATTTAAAGGGAACAGATAATTACATTTTACAAAATGTTGTCAAATTTTTGTTTAAGTTCTATCAAAATGCTGAAATTTTGTCAAA[A/T]
TTCCATCAAATTCAGAATTTTTCCAAATTGTTATATTAGTCAATGTGCGTCATCTAATTTAAAATATACTCTCAAAAATAAAGTTCCAAAGCTACATGTA

Reverse complement sequence

TACATGTAGCTTTGGAACTTTATTTTTGAGAGTATATTTTAAATTAGATGACGCACATTGACTAATATAACAATTTGGAAAAATTCTGAATTTGATGGAA[T/A]
TTTGACAAAATTTCAGCATTTTGATAGAACTTAAACAAAAATTTGACAACATTTTGTAAAATGTAATTATCTGTTCCCTTTAAATATTAGTCAATGTGCT

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 53.90% 0.30% 0.93% 44.90% NA
All Indica  2759 46.10% 0.50% 1.12% 52.30% NA
All Japonica  1512 75.10% 0.00% 0.13% 24.74% NA
Aus  269 13.80% 0.00% 4.09% 82.16% NA
Indica I  595 48.70% 0.80% 1.68% 48.74% NA
Indica II  465 30.80% 1.10% 0.22% 67.96% NA
Indica III  913 60.40% 0.20% 0.77% 38.66% NA
Indica Intermediate  786 36.60% 0.10% 1.65% 61.58% NA
Temperate Japonica  767 62.50% 0.00% 0.26% 37.29% NA
Tropical Japonica  504 94.60% 0.00% 0.00% 5.36% NA
Japonica Intermediate  241 74.70% 0.00% 0.00% 25.31% NA
VI/Aromatic  96 51.00% 0.00% 0.00% 48.96% NA
Intermediate  90 58.90% 0.00% 0.00% 41.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1003086515 A -> T LOC_Os10g06070.1 upstream_gene_variant ; 4513.0bp to feature; MODIFIER silent_mutation Average:15.808; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg1003086515 A -> T LOC_Os10g06080.1 upstream_gene_variant ; 1314.0bp to feature; MODIFIER silent_mutation Average:15.808; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg1003086515 A -> T LOC_Os10g06090.1 upstream_gene_variant ; 4081.0bp to feature; MODIFIER silent_mutation Average:15.808; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg1003086515 A -> T LOC_Os10g06080-LOC_Os10g06090 intergenic_region ; MODIFIER silent_mutation Average:15.808; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N
vg1003086515 A -> DEL N N silent_mutation Average:15.808; most accessible tissue: Minghui63 panicle, score: 25.313 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1003086515 5.78E-07 NA mr1538 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
vg1003086515 1.76E-09 2.31E-11 mr1538 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
vg1003086515 4.42E-19 1.78E-20 mr1547 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
vg1003086515 7.76E-15 2.09E-21 mr1547 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
vg1003086515 NA 1.47E-06 mr1585 Jap_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
vg1003086515 1.50E-22 1.29E-41 mr1709 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
vg1003086515 6.63E-26 3.24E-49 mr1709 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
vg1003086515 NA 6.30E-06 mr1807 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
vg1003086515 NA 8.61E-06 mr1100_2 Jap_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
vg1003086515 NA 8.76E-08 mr1129_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
vg1003086515 NA 9.23E-06 mr1255_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
vg1003086515 NA 7.25E-07 mr1257_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
vg1003086515 2.55E-06 4.51E-12 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
vg1003086515 1.90E-10 1.42E-15 mr1547_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
vg1003086515 5.30E-12 2.11E-19 mr1547_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
vg1003086515 3.45E-37 8.58E-84 mr1709_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
vg1003086515 6.03E-36 7.97E-74 mr1709_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
vg1003086515 1.30E-06 2.77E-15 mr1709_2 Jap_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
vg1003086515 NA 9.79E-07 mr1807_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