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Detailed information for vg0200790846:

Variant ID: vg0200790846 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 790846
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCTGGAATTTCAACTGGCCTAAGAATTGTGATCAAGCTAAGCTTGAACTAACCCAAAGCTAAGTACTCTCTGTAACTGCTAATTACCAATTAGAGAGG[G/A]
GACTAGACTAGGCTAGAATTCACAATTGTGAAGAGGGATGCATTGGTGAATGCAGCAATGTGCATTCACAGTAGAGACAGAGAGAAGCAAAAAGCTCACC

Reverse complement sequence

GGTGAGCTTTTTGCTTCTCTCTGTCTCTACTGTGAATGCACATTGCTGCATTCACCAATGCATCCCTCTTCACAATTGTGAATTCTAGCCTAGTCTAGTC[C/T]
CCTCTCTAATTGGTAATTAGCAGTTACAGAGAGTACTTAGCTTTGGGTTAGTTCAAGCTTAGCTTGATCACAATTCTTAGGCCAGTTGAAATTCCAGCCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.10% 18.90% 0.00% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 45.00% 55.00% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 17.30% 82.70% 0.00% 0.00% NA
Tropical Japonica  504 90.90% 9.10% 0.00% 0.00% NA
Japonica Intermediate  241 37.30% 62.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0200790846 G -> A LOC_Os02g02360.1 downstream_gene_variant ; 1611.0bp to feature; MODIFIER silent_mutation Average:68.644; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N
vg0200790846 G -> A LOC_Os02g02380.1 downstream_gene_variant ; 4220.0bp to feature; MODIFIER silent_mutation Average:68.644; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N
vg0200790846 G -> A LOC_Os02g02370.1 intron_variant ; MODIFIER silent_mutation Average:68.644; most accessible tissue: Zhenshan97 root, score: 81.772 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200790846 NA 4.81E-06 mr1002 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
vg0200790846 NA 5.26E-06 mr1154 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
vg0200790846 NA 1.61E-09 mr1002_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
vg0200790846 NA 8.84E-06 mr1330_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
vg0200790846 NA 1.27E-07 mr1347_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