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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0918876795:

Variant ID: vg0918876795 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 18876795
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGAAAAAAGAACCAAACCAAAACAAACCATGCATGATCATGACTAACAAATCAGAGATCAAAATCAAACTCCAAGACACGGCCCAAATCAAGAACAAG[A/G]
AAGAGACACACATATATATGCATCAAACAAATCAGAGAGAGAGAGAGAGAGGGAGAGAGATTCAGTAAACAAAGCCGTACATGAAGCTTGCGGCAGCGGC

Reverse complement sequence

GCCGCTGCCGCAAGCTTCATGTACGGCTTTGTTTACTGAATCTCTCTCCCTCTCTCTCTCTCTCTCTGATTTGTTTGATGCATATATATGTGTGTCTCTT[T/C]
CTTGTTCTTGATTTGGGCCGTGTCTTGGAGTTTGATTTTGATCTCTGATTTGTTAGTCATGATCATGCATGGTTTGTTTTGGTTTGGTTCTTTTTTCTTG

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 92.30% 7.60% 0.06% 0.00% NA
All Indica  2759 98.50% 1.50% 0.04% 0.00% NA
All Japonica  1512 92.90% 7.00% 0.07% 0.00% NA
Aus  269 49.40% 50.20% 0.37% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 98.60% 1.30% 0.11% 0.00% NA
Indica Intermediate  786 96.90% 3.10% 0.00% 0.00% NA
Temperate Japonica  767 92.70% 7.20% 0.13% 0.00% NA
Tropical Japonica  504 90.50% 9.50% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0918876795 A -> G LOC_Os09g31390.3 upstream_gene_variant ; 2355.0bp to feature; MODIFIER silent_mutation Average:40.434; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N
vg0918876795 A -> G LOC_Os09g31390.1 intron_variant ; MODIFIER silent_mutation Average:40.434; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N
vg0918876795 A -> G LOC_Os09g31390.2 intron_variant ; MODIFIER silent_mutation Average:40.434; most accessible tissue: Zhenshan97 young leaf, score: 70.625 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0918876795 NA 6.82E-06 mr1230_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
vg0918876795 9.48E-07 4.91E-08 mr1252_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
vg0918876795 6.39E-06 1.02E-06 mr1263_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
vg0918876795 NA 1.21E-06 mr1405_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
vg0918876795 2.52E-06 NA mr1567_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
vg0918876795 2.82E-06 NA mr1591_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
vg0918876795 2.46E-06 NA mr1594_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
vg0918876795 5.95E-06 NA mr1596_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
vg0918876795 NA 7.62E-07 mr1597_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
vg0918876795 NA 9.59E-06 mr1661_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
vg0918876795 6.96E-06 6.52E-08 mr1729_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
vg0918876795 NA 8.75E-06 mr1736_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
vg0918876795 NA 3.71E-06 mr1740_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