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Detailed information for vg0608086564:

Variant ID: vg0608086564 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 8086564
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTAATGTTTGCATTCCTTTGGTTGGCTTGCTCAACAACATAGGAAAAATTCCTGTGTTTTTCAATCCATAGGTTTGCACATGTATTCCTGTAGTATTC[C/T]
TACGTTTTTCCTGTTCCTACGTTTTGAAAATCCTGTGTACCGAACGAGCCCTAAGCTAAACAAAAGAGGATGGAGTGGATGTTTTCATTCCTATGGAATT

Reverse complement sequence

AATTCCATAGGAATGAAAACATCCACTCCATCCTCTTTTGTTTAGCTTAGGGCTCGTTCGGTACACAGGATTTTCAAAACGTAGGAACAGGAAAAACGTA[G/A]
GAATACTACAGGAATACATGTGCAAACCTATGGATTGAAAAACACAGGAATTTTTCCTATGTTGTTGAGCAAGCCAACCAAAGGAATGCAAACATTAGGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.20% 6.40% 5.61% 5.76% NA
All Indica  2759 99.00% 0.10% 0.18% 0.72% NA
All Japonica  1512 51.50% 19.00% 16.07% 13.43% NA
Aus  269 94.80% 0.40% 1.49% 3.35% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.20% 0.00% 0.43% NA
Indica III  913 98.80% 0.00% 0.11% 1.10% NA
Indica Intermediate  786 98.20% 0.30% 0.51% 1.02% NA
Temperate Japonica  767 62.80% 8.30% 17.60% 11.21% NA
Tropical Japonica  504 30.40% 37.50% 14.09% 18.06% NA
Japonica Intermediate  241 59.80% 14.10% 15.35% 10.79% NA
VI/Aromatic  96 58.30% 4.20% 4.17% 33.33% NA
Intermediate  90 72.20% 8.90% 10.00% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0608086564 C -> T LOC_Os06g14430-LOC_Os06g14440 intergenic_region ; MODIFIER silent_mutation Average:50.731; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N
vg0608086564 C -> DEL N N silent_mutation Average:50.731; most accessible tissue: Minghui63 flag leaf, score: 73.334 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608086564 NA 9.82E-07 mr1195_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
vg0608086564 7.89E-10 NA mr1238_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
vg0608086564 5.98E-06 NA mr1310_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
vg0608086564 NA 5.45E-07 mr1321_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
vg0608086564 NA 4.82E-07 mr1358_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
vg0608086564 8.02E-10 2.65E-25 mr1484_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
vg0608086564 8.20E-07 NA mr1841_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
vg0608086564 7.76E-08 7.74E-20 mr1900_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
vg0608086564 1.46E-09 3.42E-22 mr1945_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
vg0608086564 9.33E-06 NA mr1959_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
vg0608086564 NA 8.87E-06 mr1959_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