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Detailed information for vg0410073312:

Variant ID: vg0410073312 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10073312
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:


AATTTTTAGAGTTAATATGAATTCTTTATGTATTTTACAAGTTATAACATGTTATAGGTGTATAGTGTTATATAGGTTCATGGCTTTAGAGGTTTAGGTC[C/T]
AGAACTTGCCTCATCTAGCCAGTGATGTATAAAATGAGTATTTTAGTTAACTAATCTAATCTTAGTTCATAATTTTAGAGTTTATATTATTTTACTACAC

Reverse complement sequence

GTGTAGTAAAATAATATAAACTCTAAAATTATGAACTAAGATTAGATTAGTTAACTAAAATACTCATTTTATACATCACTGGCTAGATGAGGCAAGTTCT[G/A]
GACCTAAACCTCTAAAGCCATGAACCTATATAACACTATACACCTATAACATGTTATAACTTGTAAAATACATAAAGAATTCATATTAACTCTAAAAATT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.70% 27.20% 0.04% 0.00% NA
All Indica  2759 53.70% 46.20% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 24.00% 76.00% 0.00% 0.00% NA
Indica II  465 74.80% 25.20% 0.00% 0.00% NA
Indica III  913 59.30% 40.70% 0.00% 0.00% NA
Indica Intermediate  786 57.30% 42.60% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 88.90% 10.00% 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
vg0410073312 C -> T LOC_Os04g18200-LOC_Os04g18230 intergenic_region ; MODIFIER silent_mutation Average:45.798; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410073312 NA 1.47E-06 mr1386 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
vg0410073312 NA 7.19E-10 mr1403 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
vg0410073312 NA 3.75E-07 mr1403 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
vg0410073312 NA 3.29E-06 mr1608 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
vg0410073312 NA 4.08E-08 mr1830 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
vg0410073312 4.03E-09 NA mr1846 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
vg0410073312 4.97E-09 1.20E-13 mr1846 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
vg0410073312 1.05E-06 NA mr1830_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
vg0410073312 3.78E-06 3.62E-12 mr1830_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
vg0410073312 1.58E-14 4.84E-16 mr1846_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
vg0410073312 7.73E-13 1.20E-28 mr1846_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