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Detailed information for vg0410847838:

Variant ID: vg0410847838 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 10847838
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


CACCACCTTCTCCAGATTCCCCGCCATTACTGTAAACGGAGCCCAGGCAACAGTTTGGTTGAGGATTGGCACGAATTCCGCTGTTGACTGGGACATGGCA[G/A]
AGGAGGAAGACGGAGAATGGCTGGAGGAGCGGAGAATCAAGGGGCTATTTTGTTGGATTTACCCTGAGAGCAAAACCCTAAATCGCCGGAAGCAAAGAGC

Reverse complement sequence

GCTCTTTGCTTCCGGCGATTTAGGGTTTTGCTCTCAGGGTAAATCCAACAAAATAGCCCCTTGATTCTCCGCTCCTCCAGCCATTCTCCGTCTTCCTCCT[C/T]
TGCCATGTCCCAGTCAACAGCGGAATTCGTGCCAATCCTCAACCAAACTGTTGCCTGGGCTCCGTTTACAGTAATGGCGGGGAATCTGGAGAAGGTGGTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 72.60% 27.40% 0.00% 0.00% NA
All Indica  2759 53.50% 46.50% 0.00% 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 23.40% 76.60% 0.00% 0.00% NA
Indica II  465 74.80% 25.20% 0.00% 0.00% NA
Indica III  913 59.10% 40.90% 0.00% 0.00% NA
Indica Intermediate  786 57.00% 43.00% 0.00% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0410847838 G -> A LOC_Os04g19480.1 synonymous_variant ; p.Leu121Leu; LOW synonymous_codon Average:55.786; most accessible tissue: Zhenshan97 young leaf, score: 90.27 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0410847838 NA 2.54E-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
vg0410847838 NA 1.16E-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
vg0410847838 NA 4.49E-08 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
vg0410847838 NA 4.55E-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
vg0410847838 8.36E-07 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
vg0410847838 2.20E-06 1.23E-11 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
vg0410847838 NA 6.68E-06 mr1304_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
vg0410847838 8.50E-08 NA mr1830_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
vg0410847838 3.98E-07 1.46E-13 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
vg0410847838 2.27E-14 2.87E-16 mr1846_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
vg0410847838 1.65E-12 5.54E-30 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