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Detailed information for vg0205136369:

Variant ID: vg0205136369 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5136369
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


CGTCGCGCGAAGCATATCGAGATTGACATTCACTTTGTTTCTGAGAAGGTTGCTTTGGGGCAGGTTCATGTGCTACATGTCCTGTCTTCTCACCAGTTTG[C/T]
GTACATCATGACCAAAAGCCTACCTATTTAGTTATTTACTGATTTTAGGTCGAGTCTTTGCGTTTGTGATCCTCCCGTTGCAAATGCGGGCGGGTATTGG

Reverse complement sequence

CCAATACCCGCCCGCATTTGCAACGGGAGGATCACAAACGCAAAGACTCGACCTAAAATCAGTAAATAACTAAATAGGTAGGCTTTTGGTCATGATGTAC[G/A]
CAAACTGGTGAGAAGACAGGACATGTAGCACATGAACCTGCCCCAAAGCAACCTTCTCAGAAACAAAGTGAATGTCAATCTCGATATGCTTCGCGCGACG

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 95.20% 3.00% 1.82% 0.00% NA
All Indica  2759 92.00% 5.00% 3.01% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 84.00% 8.70% 7.23% 0.00% NA
Indica II  465 88.60% 10.30% 1.08% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 90.80% 4.70% 4.45% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 0.00% 2.22% 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
vg0205136369 C -> T LOC_Os02g09910.1 downstream_gene_variant ; 3740.0bp to feature; MODIFIER silent_mutation Average:51.179; most accessible tissue: Minghui63 flag leaf, score: 65.44 N N N N
vg0205136369 C -> T LOC_Os02g09910-LOC_Os02g09920 intergenic_region ; MODIFIER silent_mutation Average:51.179; most accessible tissue: Minghui63 flag leaf, score: 65.44 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205136369 NA 7.90E-07 mr1038 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
vg0205136369 NA 2.15E-06 mr1038 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
vg0205136369 NA 4.55E-10 mr1389 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
vg0205136369 NA 2.49E-08 mr1389 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
vg0205136369 NA 4.20E-06 mr1909 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
vg0205136369 NA 7.00E-09 mr1038_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
vg0205136369 NA 1.26E-07 mr1038_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
vg0205136369 9.60E-06 9.63E-06 mr1273_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
vg0205136369 1.05E-06 1.05E-06 mr1273_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
vg0205136369 NA 1.58E-07 mr1389_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
vg0205136369 NA 8.78E-07 mr1389_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