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Detailed information for vg0324385736:

Variant ID: vg0324385736 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24385736
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GCAGCAGTCCCCACCCGGCCACCTTCACATGTTTTAAGCTGTTTTTAGCAAAGTGGCTTGTTTTAAAATAAAGTTATTTTTTCATCTAGCTCTTATCTCA[A/C]
CAAATCAGAACTATTATCTATTTAACTTTTTCACCTACTTTATCTTATCAACCAATCACATTATTCCTCTAATTATTTTCATCGTACTTTGTTAATACCT

Reverse complement sequence

AGGTATTAACAAAGTACGATGAAAATAATTAGAGGAATAATGTGATTGGTTGATAAGATAAAGTAGGTGAAAAAGTTAAATAGATAATAGTTCTGATTTG[T/G]
TGAGATAAGAGCTAGATGAAAAAATAACTTTATTTTAAAACAAGCCACTTTGCTAAAAACAGCTTAAAACATGTGAAGGTGGCCGGGTGGGGACTGCTGC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 99.50% 0.30% 0.19% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 98.70% 0.80% 0.53% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 97.50% 1.60% 0.91% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0324385736 A -> C LOC_Os03g43620.1 downstream_gene_variant ; 3793.0bp to feature; MODIFIER N Average:49.444; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N
vg0324385736 A -> C LOC_Os03g43610-LOC_Os03g43620 intergenic_region ; MODIFIER N Average:49.444; most accessible tissue: Zhenshan97 panicle, score: 68.538 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324385736 NA 2.41E-07 mr1028 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
vg0324385736 NA 3.83E-06 mr1245 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
vg0324385736 7.95E-06 7.95E-06 mr1369 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
vg0324385736 NA 1.42E-06 mr1453 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
vg0324385736 NA 9.07E-08 mr1648 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
vg0324385736 NA 1.34E-06 mr1652 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
vg0324385736 1.12E-06 2.21E-09 mr1697 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