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Detailed information for vg0800413021:

Variant ID: vg0800413021 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 413021
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.03, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


CTATATTTAGAAGTCACCATTTATATCCTAGAGTTTTATGGATTCGTTGTGGTTTTGATAAAAACGGAAAGAAAAGATCGAGTGAATAAGAGCACTCAAC[C/A]
AATTTTAGGAGATTGAGAAAGATTGGATCGTATTTGATGGGGAGTATTGGTTCTGGCATCATACTACACGGTACTGTCTTCGAGGTTGAAGACGGCAGTC

Reverse complement sequence

GACTGCCGTCTTCAACCTCGAAGACAGTACCGTGTAGTATGATGCCAGAACCAATACTCCCCATCAAATACGATCCAATCTTTCTCAATCTCCTAAAATT[G/T]
GTTGAGTGCTCTTATTCACTCGATCTTTTCTTTCCGTTTTTATCAAAACCACAACGAATCCATAAAACTCTAGGATATAAATGGTGACTTCTAAATATAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.70% 45.00% 0.28% 0.00% NA
All Indica  2759 34.70% 65.00% 0.33% 0.00% NA
All Japonica  1512 86.80% 13.10% 0.07% 0.00% NA
Aus  269 92.20% 7.40% 0.37% 0.00% NA
Indica I  595 54.80% 45.20% 0.00% 0.00% NA
Indica II  465 12.90% 86.90% 0.22% 0.00% NA
Indica III  913 31.00% 68.90% 0.11% 0.00% NA
Indica Intermediate  786 36.60% 62.50% 0.89% 0.00% NA
Temperate Japonica  767 97.00% 3.00% 0.00% 0.00% NA
Tropical Japonica  504 70.60% 29.20% 0.20% 0.00% NA
Japonica Intermediate  241 88.40% 11.60% 0.00% 0.00% NA
VI/Aromatic  96 13.50% 85.40% 1.04% 0.00% NA
Intermediate  90 58.90% 40.00% 1.11% 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
vg0800413021 C -> A LOC_Os08g01690-LOC_Os08g01700 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0800413021 NA 3.32E-06 mr1279 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
vg0800413021 2.25E-13 2.60E-30 mr1746 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
vg0800413021 9.57E-11 4.95E-14 mr1746 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
vg0800413021 NA 1.81E-11 mr1746 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
vg0800413021 6.99E-11 NA mr1277_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
vg0800413021 1.43E-08 2.82E-06 mr1277_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
vg0800413021 NA 9.26E-07 mr1558_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
vg0800413021 2.17E-18 1.50E-37 mr1746_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
vg0800413021 5.56E-14 6.79E-18 mr1746_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
vg0800413021 NA 3.59E-11 mr1746_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
vg0800413021 NA 6.19E-13 mr1769_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