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Detailed information for vg0223523255:

Variant ID: vg0223523255 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 23523255
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGCCTATGCATTTAATGCATTTATTATGGAGTATGTGATAGATAGCTCTTGCATGAGAACCAACTATATTCTTTTTTTTTTCAAATTTTCTCTTATCCA[C/G]
GTAAGCTTATACTCCCTCCGTCCAAAAAAAAAGGCAAACCCTGGGTTTCCGTGTCCAACTTTAACTGTCTGTCTTATATGAAATTTTTTTATAATTCGTA

Reverse complement sequence

TACGAATTATAAAAAAATTTCATATAAGACAGACAGTTAAAGTTGGACACGGAAACCCAGGGTTTGCCTTTTTTTTTGGACGGAGGGAGTATAAGCTTAC[G/C]
TGGATAAGAGAAAATTTGAAAAAAAAAAGAATATAGTTGGTTCTCATGCAAGAGCTATCTATCACATACTCCATAATAAATGCATTAAATGCATAGGCGA

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 94.30% 4.90% 0.11% 0.72% NA
All Indica  2759 91.40% 8.40% 0.18% 0.04% NA
All Japonica  1512 99.70% 0.10% 0.00% 0.20% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 89.10% 10.80% 0.17% 0.00% NA
Indica II  465 98.90% 0.90% 0.00% 0.22% NA
Indica III  913 87.50% 12.30% 0.22% 0.00% NA
Indica Intermediate  786 93.30% 6.50% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 0.00% 1.24% NA
VI/Aromatic  96 74.00% 0.00% 0.00% 26.04% NA
Intermediate  90 94.40% 0.00% 0.00% 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
vg0223523255 C -> G LOC_Os02g38910.1 upstream_gene_variant ; 2704.0bp to feature; MODIFIER silent_mutation Average:58.156; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg0223523255 C -> G LOC_Os02g38920.1 upstream_gene_variant ; 4263.0bp to feature; MODIFIER silent_mutation Average:58.156; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg0223523255 C -> G LOC_Os02g38910-LOC_Os02g38920 intergenic_region ; MODIFIER silent_mutation Average:58.156; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg0223523255 C -> DEL N N silent_mutation Average:58.156; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0223523255 3.32E-06 3.33E-06 mr1192_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
vg0223523255 6.66E-06 4.04E-06 mr1278_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
vg0223523255 3.63E-06 3.63E-06 mr1312_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
vg0223523255 6.56E-06 6.56E-06 mr1337_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
vg0223523255 1.60E-06 1.60E-06 mr1374_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
vg0223523255 3.69E-06 3.69E-06 mr1524_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
vg0223523255 1.25E-06 1.54E-06 mr1645_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
vg0223523255 8.18E-06 2.61E-07 mr1648_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
vg0223523255 9.52E-07 9.52E-07 mr1663_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
vg0223523255 4.50E-06 4.50E-06 mr1697_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
vg0223523255 5.33E-06 5.33E-06 mr1979_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