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Detailed information for vg0106427492:

Variant ID: vg0106427492 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6427492
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: 259. )

Flanking Sequence (100 bp) in Reference Genome:


AATCGTGACTACCAGCGGTATGCTTTGTTGGAAGGTACAACATCTCAATATTTTGCTATTACTTTTGAAGAACCATTAACAAAATGTATGTGTAATCTTT[G/A]
TTAAAATGGATGCAGAAGTGAGAAACTCCTTGTTGAAAGAACCAACCCTGCATGACGCCATTAAGATTGTTGTGACCTATAGGAAGCAAGAGCTACTGCA

Reverse complement sequence

TGCAGTAGCTCTTGCTTCCTATAGGTCACAACAATCTTAATGGCGTCATGCAGGGTTGGTTCTTTCAACAAGGAGTTTCTCACTTCTGCATCCATTTTAA[C/T]
AAAGATTACACATACATTTTGTTAATGGTTCTTCAAAAGTAATAGCAAAATATTGAGATGTTGTACCTTCCAACAAAGCATACCGCTGGTAGTCACGATT

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 90.50% 9.40% 0.08% 0.00% NA
All Indica  2759 92.30% 7.70% 0.00% 0.00% NA
All Japonica  1512 85.20% 14.70% 0.13% 0.00% NA
Aus  269 97.80% 1.50% 0.74% 0.00% NA
Indica I  595 89.90% 10.10% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 82.40% 17.60% 0.00% 0.00% NA
Temperate Japonica  767 98.60% 1.30% 0.13% 0.00% NA
Tropical Japonica  504 78.60% 21.20% 0.20% 0.00% NA
Japonica Intermediate  241 56.40% 43.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0106427492 G -> A LOC_Os01g11880.1 upstream_gene_variant ; 4844.0bp to feature; MODIFIER silent_mutation Average:24.662; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N
vg0106427492 G -> A LOC_Os01g11870.1 intron_variant ; MODIFIER silent_mutation Average:24.662; most accessible tissue: Zhenshan97 panicle, score: 39.652 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106427492 NA 9.53E-06 mr1519_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
vg0106427492 NA 1.04E-08 mr1533_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
vg0106427492 NA 7.26E-06 mr1580_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
vg0106427492 NA 6.19E-07 mr1825_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
vg0106427492 NA 1.27E-06 mr1870_2 Ind_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
vg0106427492 NA 2.27E-07 mr1924_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
vg0106427492 NA 6.11E-08 mr1943_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
vg0106427492 NA 3.60E-06 mr1980_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