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Detailed information for vg0609841754:

Variant ID: vg0609841754 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 9841754
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


AAATTGACCCTGCCATATACATTTTTTTAAGAACTTCTCAAATTTACCAAAACAAGGAAGCACACAAACTCAATTTGAAAAAAATAATATGCAAGTCTAA[A/T]
GATTTTTTTTTTTTAAAAGCAAGTCAGTAATTGCAATTGTTTTCAATTAGAATTTATGAAAACAAAACAATAGAACGAGCATAAAAGAATGAACAATGCA

Reverse complement sequence

TGCATTGTTCATTCTTTTATGCTCGTTCTATTGTTTTGTTTTCATAAATTCTAATTGAAAACAATTGCAATTACTGACTTGCTTTTAAAAAAAAAAAATC[T/A]
TTAGACTTGCATATTATTTTTTTCAAATTGAGTTTGTGTGCTTCCTTGTTTTGGTAAATTTGAGAAGTTCTTAAAAAAATGTATATGGCAGGGTCAATTT

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 87.60% 1.10% 8.10% 3.22% NA
All Indica  2759 88.10% 0.00% 8.19% 3.66% NA
All Japonica  1512 84.90% 3.40% 8.99% 2.71% NA
Aus  269 93.30% 0.00% 4.46% 2.23% NA
Indica I  595 90.10% 0.00% 8.74% 1.18% NA
Indica II  465 83.90% 0.00% 11.61% 4.52% NA
Indica III  913 90.90% 0.00% 4.16% 4.93% NA
Indica Intermediate  786 86.00% 0.00% 10.43% 3.56% NA
Temperate Japonica  767 84.50% 6.60% 8.34% 0.52% NA
Tropical Japonica  504 86.30% 0.00% 8.53% 5.16% NA
Japonica Intermediate  241 83.40% 0.00% 12.03% 4.56% NA
VI/Aromatic  96 95.80% 0.00% 0.00% 4.17% NA
Intermediate  90 90.00% 0.00% 10.00% 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
vg0609841754 A -> T LOC_Os06g16970.1 upstream_gene_variant ; 3703.0bp to feature; MODIFIER silent_mutation Average:41.356; most accessible tissue: Callus, score: 85.785 N N N N
vg0609841754 A -> T LOC_Os06g16980.1 intron_variant ; MODIFIER silent_mutation Average:41.356; most accessible tissue: Callus, score: 85.785 N N N N
vg0609841754 A -> T LOC_Os06g16980.2 intron_variant ; MODIFIER silent_mutation Average:41.356; most accessible tissue: Callus, score: 85.785 N N N N
vg0609841754 A -> DEL N N silent_mutation Average:41.356; most accessible tissue: Callus, score: 85.785 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0609841754 3.68E-08 1.03E-10 mr1210 Jap_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
vg0609841754 1.65E-08 9.03E-11 mr1305 Jap_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
vg0609841754 NA 1.98E-06 mr1515 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
vg0609841754 1.55E-08 4.77E-13 mr1585 Jap_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
vg0609841754 4.10E-07 8.17E-10 mr1586 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
vg0609841754 6.15E-07 6.15E-07 mr1649 Jap_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
vg0609841754 NA 2.29E-07 mr1765 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
vg0609841754 1.19E-10 8.88E-13 mr1305_2 Jap_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
vg0609841754 8.34E-07 1.35E-08 mr1409_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
vg0609841754 5.02E-07 5.55E-08 mr1559_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
vg0609841754 2.34E-11 4.15E-15 mr1585_2 Jap_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
vg0609841754 3.69E-06 3.61E-07 mr1703_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
vg0609841754 NA 7.92E-07 mr1765_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