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Detailed information for vg0608454378:

Variant ID: vg0608454378 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 8454378
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GTTAGGGGACGATTTTGTATCTCGATGATAAGTTGAGGCACCTTACGTGTACTTTTTCCTATTTTTGCTCCACCTATTCTTATTTGGATGGATTCTATTG[G/A]
GGAATAAGTCCATTTTACCTTCCTTTATCTCTTTGCTCCTGGTTGAATCGTCTCCTGTAACCGTAAAACCGGATATAATTAACATCACCCCTCGTCTTAA

Reverse complement sequence

TTAAGACGAGGGGTGATGTTAATTATATCCGGTTTTACGGTTACAGGAGACGATTCAACCAGGAGCAAAGAGATAAAGGAAGGTAAAATGGACTTATTCC[C/T]
CAATAGAATCCATCCAAATAAGAATAGGTGGAGCAAAAATAGGAAAAAGTACACGTAAGGTGCCTCAACTTATCATCGAGATACAAAATCGTCCCCTAAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.70% 26.70% 0.61% 5.99% NA
All Indica  2759 87.00% 2.60% 0.36% 10.08% NA
All Japonica  1512 38.40% 60.60% 0.99% 0.00% NA
Aus  269 15.20% 84.80% 0.00% 0.00% NA
Indica I  595 82.70% 1.00% 0.84% 15.46% NA
Indica II  465 94.60% 3.40% 0.00% 1.94% NA
Indica III  913 89.30% 1.50% 0.22% 8.98% NA
Indica Intermediate  786 83.00% 4.60% 0.38% 12.09% NA
Temperate Japonica  767 51.20% 47.80% 0.91% 0.00% NA
Tropical Japonica  504 22.40% 77.20% 0.40% 0.00% NA
Japonica Intermediate  241 31.10% 66.40% 2.49% 0.00% NA
VI/Aromatic  96 84.40% 13.50% 2.08% 0.00% NA
Intermediate  90 55.60% 36.70% 2.22% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0608454378 G -> A LOC_Os06g14870.1 upstream_gene_variant ; 287.0bp to feature; MODIFIER silent_mutation Average:53.414; most accessible tissue: Zhenshan97 young leaf, score: 76.773 N N N N
vg0608454378 G -> A LOC_Os06g14890.1 downstream_gene_variant ; 2447.0bp to feature; MODIFIER silent_mutation Average:53.414; most accessible tissue: Zhenshan97 young leaf, score: 76.773 N N N N
vg0608454378 G -> A LOC_Os06g14870-LOC_Os06g14890 intergenic_region ; MODIFIER silent_mutation Average:53.414; most accessible tissue: Zhenshan97 young leaf, score: 76.773 N N N N
vg0608454378 G -> DEL N N silent_mutation Average:53.414; most accessible tissue: Zhenshan97 young leaf, score: 76.773 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0608454378 NA 7.13E-10 mr1299 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
vg0608454378 NA 6.36E-07 mr1345 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
vg0608454378 NA 2.97E-08 mr1648 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
vg0608454378 NA 1.65E-08 mr1666 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
vg0608454378 NA 1.14E-10 mr1696 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
vg0608454378 NA 8.59E-09 mr1756 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
vg0608454378 NA 5.93E-12 mr1938 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
vg0608454378 5.67E-06 NA mr1068_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
vg0608454378 NA 2.15E-11 mr1138_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
vg0608454378 NA 6.21E-15 mr1552_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
vg0608454378 1.14E-06 NA mr1617_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
vg0608454378 NA 8.83E-13 mr1666_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
vg0608454378 NA 1.80E-08 mr1696_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
vg0608454378 NA 7.61E-11 mr1761_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