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Detailed information for vg0214881617:

Variant ID: vg0214881617 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 14881617
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


CGCATCAAGGCGTAGGGTGCCAGGAGCAGCACTTCGACCTTGGGTTTGGTTTATGCCGGGCTTTACAACTAACGGTTCGATGTTGGGGATAGAAAACCGT[G/C]
AACGTCCCCACGGAAGGCGTAAAGTTCCAACCGGCGGCTTTTTAGTGGCTAAAGGGTAATTGGGATAAAAGAAAATATTTGAAAAGTCAAATATAAATTC

Reverse complement sequence

GAATTTATATTTGACTTTTCAAATATTTTCTTTTATCCCAATTACCCTTTAGCCACTAAAAAGCCGCCGGTTGGAACTTTACGCCTTCCGTGGGGACGTT[C/G]
ACGGTTTTCTATCCCCAACATCGAACCGTTAGTTGTAAAGCCCGGCATAAACCAAACCCAAGGTCGAAGTGCTGCTCCTGGCACCCTACGCCTTGATGCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.00% 7.30% 1.69% 0.00% NA
All Indica  2759 85.00% 12.30% 2.65% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 98.50% 0.00% 1.49% 0.00% NA
Indica I  595 96.10% 0.00% 3.87% 0.00% NA
Indica II  465 70.50% 24.90% 4.52% 0.00% NA
Indica III  913 80.60% 18.30% 1.10% 0.00% NA
Indica Intermediate  786 90.30% 7.30% 2.42% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 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 92.20% 5.60% 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
vg0214881617 G -> C LOC_Os02g25490.1 upstream_gene_variant ; 975.0bp to feature; MODIFIER silent_mutation Average:72.191; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N
vg0214881617 G -> C LOC_Os02g25480.1 downstream_gene_variant ; 2139.0bp to feature; MODIFIER silent_mutation Average:72.191; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N
vg0214881617 G -> C LOC_Os02g25480-LOC_Os02g25490 intergenic_region ; MODIFIER silent_mutation Average:72.191; most accessible tissue: Zhenshan97 panicle, score: 83.904 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0214881617 NA 2.81E-06 mr1074 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
vg0214881617 NA 3.62E-07 mr1109 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
vg0214881617 NA 2.34E-06 mr1129 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
vg0214881617 NA 1.08E-07 mr1130 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
vg0214881617 NA 1.32E-09 mr1317 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
vg0214881617 NA 3.25E-06 mr1818 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
vg0214881617 3.74E-08 8.53E-18 mr1855 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
vg0214881617 1.53E-07 5.21E-19 mr1855 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
vg0214881617 3.10E-06 NA mr1897 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
vg0214881617 NA 2.13E-09 mr1934 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
vg0214881617 NA 1.25E-06 mr1050_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
vg0214881617 NA 8.54E-07 mr1253_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
vg0214881617 NA 1.65E-11 mr1317_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
vg0214881617 NA 3.05E-06 mr1332_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
vg0214881617 NA 8.67E-10 mr1338_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
vg0214881617 NA 1.31E-06 mr1428_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
vg0214881617 NA 6.01E-06 mr1610_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
vg0214881617 NA 3.10E-07 mr1818_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
vg0214881617 5.93E-09 NA mr1855_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
vg0214881617 2.43E-08 2.03E-15 mr1855_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
vg0214881617 NA 2.64E-09 mr1897_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
vg0214881617 NA 2.80E-11 mr1914_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
vg0214881617 NA 7.74E-08 mr1927_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