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Detailed information for vg1124122024:

Variant ID: vg1124122024 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24122024
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.60, C: 0.39, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


CATTTTGGGTATTGTTCTTTTCTTTAGGCATCAATTTATCATACCTTTCCTGTAGAGACTCACAGCCTTTAAGAATATCATCGTGAGCAAGTGTCACGGC[T/C]
TCTTGAAAAATCATATTGGGCACAAAAAAGCTGTCAGGGATCAGGTCAGGCTTTGAAACCAGTAGATATGCACAGTATCGCGACAAGCTATTCGCGATGA

Reverse complement sequence

TCATCGCGAATAGCTTGTCGCGATACTGTGCATATCTACTGGTTTCAAAGCCTGACCTGATCCCTGACAGCTTTTTTGTGCCCAATATGATTTTTCAAGA[A/G]
GCCGTGACACTTGCTCACGATGATATTCTTAAAGGCTGTGAGTCTCTACAGGAAAGGTATGATAAATTGATGCCTAAAGAAAAGAACAATACCCAAAATG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.40% 28.60% 0.00% 0.00% NA
All Indica  2759 72.30% 27.70% 0.00% 0.00% NA
All Japonica  1512 69.00% 31.00% 0.00% 0.00% NA
Aus  269 91.10% 8.90% 0.00% 0.00% NA
Indica I  595 95.60% 4.40% 0.00% 0.00% NA
Indica II  465 74.40% 25.60% 0.00% 0.00% NA
Indica III  913 56.20% 43.80% 0.00% 0.00% NA
Indica Intermediate  786 72.00% 28.00% 0.00% 0.00% NA
Temperate Japonica  767 84.00% 16.00% 0.00% 0.00% NA
Tropical Japonica  504 51.00% 49.00% 0.00% 0.00% NA
Japonica Intermediate  241 59.30% 40.70% 0.00% 0.00% NA
VI/Aromatic  96 31.20% 68.80% 0.00% 0.00% NA
Intermediate  90 67.80% 32.20% 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
vg1124122024 T -> C LOC_Os11g40450.1 synonymous_variant ; p.Glu1872Glu; LOW synonymous_codon Average:48.836; most accessible tissue: Callus, score: 78.651 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124122024 NA 5.41E-06 mr1047 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
vg1124122024 NA 3.24E-06 mr1063 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
vg1124122024 NA 3.38E-08 mr1133 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
vg1124122024 NA 9.88E-09 mr1242 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
vg1124122024 NA 1.74E-06 mr1133_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
vg1124122024 NA 9.29E-07 mr1242_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
vg1124122024 NA 7.97E-06 mr1246_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