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Detailed information for vg0904833940:

Variant ID: vg0904833940 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4833940
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, C: 0.02, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:


AAATTCTAGGAGAGAACTCCGATACTTTGGGGCACTCCTTCCGAGCTTCCCCTCACACTATTACTAAACTGACATACTAAAGTAAAGCTAACAAGTGAGT[G/C]
GTACTCTACTTGAGATCAAGTTGCATGTTTTCCAACTGTGAAGGCCTCCTCGTTACATAGTGTGCCAATGACAGTTGGAATGGTGGCTAGGGAGGTCGAT

Reverse complement sequence

ATCGACCTCCCTAGCCACCATTCCAACTGTCATTGGCACACTATGTAACGAGGAGGCCTTCACAGTTGGAAAACATGCAACTTGATCTCAAGTAGAGTAC[C/G]
ACTCACTTGTTAGCTTTACTTTAGTATGTCAGTTTAGTAATAGTGTGAGGGGAAGCTCGGAAGGAGTGCCCCAAAGTATCGGAGTTCTCTCCTAGAATTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.30% 37.00% 0.13% 13.58% NA
All Indica  2759 80.60% 15.70% 0.11% 3.62% NA
All Japonica  1512 2.90% 73.40% 0.07% 23.61% NA
Aus  269 1.90% 49.80% 0.37% 47.96% NA
Indica I  595 66.70% 32.80% 0.00% 0.50% NA
Indica II  465 84.90% 12.00% 0.00% 3.01% NA
Indica III  913 89.00% 7.90% 0.11% 2.96% NA
Indica Intermediate  786 78.80% 13.90% 0.25% 7.12% NA
Temperate Japonica  767 0.80% 98.30% 0.00% 0.91% NA
Tropical Japonica  504 5.60% 40.50% 0.20% 53.77% NA
Japonica Intermediate  241 4.10% 63.10% 0.00% 32.78% NA
VI/Aromatic  96 11.50% 41.70% 0.00% 46.88% NA
Intermediate  90 50.00% 36.70% 1.11% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0904833940 G -> DEL N N silent_mutation Average:45.795; most accessible tissue: Zhenshan97 young leaf, score: 73.923 N N N N
vg0904833940 G -> C LOC_Os09g09060.1 downstream_gene_variant ; 574.0bp to feature; MODIFIER silent_mutation Average:45.795; most accessible tissue: Zhenshan97 young leaf, score: 73.923 N N N N
vg0904833940 G -> C LOC_Os09g09050-LOC_Os09g09060 intergenic_region ; MODIFIER silent_mutation Average:45.795; most accessible tissue: Zhenshan97 young leaf, score: 73.923 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904833940 NA 4.17E-09 mr1201 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
vg0904833940 NA 6.76E-09 mr1219 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
vg0904833940 NA 4.80E-09 mr1274 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
vg0904833940 NA 2.44E-14 mr1301 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
vg0904833940 NA 8.82E-06 mr1189_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
vg0904833940 NA 3.41E-06 mr1201_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
vg0904833940 NA 3.48E-06 mr1219_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
vg0904833940 NA 2.27E-07 mr1274_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
vg0904833940 NA 4.11E-09 mr1277_2 Jap_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
vg0904833940 NA 2.49E-15 mr1301_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
vg0904833940 NA 1.69E-11 mr1410_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
vg0904833940 NA 4.25E-06 mr1471_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