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Detailed information for vg1126219428:

Variant ID: vg1126219428 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26219428
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CCAACCGATGTTTTGATGCTCTTCTCGCTCAAAGATTTGTTCTTCCTGGTGATGTTGGAAATTCAGGCAAGGTAAACAGCTGCAGAGTGCACAATCTAGT[C/A]
CGTGACTTCATTGCCTGGGTCATCAGAGATGACAACTTTGTGTACACAAAGCTACCAGTCGACTTGGCTCACCGTCTTCCCATCCACAATGGAGAAAGAC

Reverse complement sequence

GTCTTTCTCCATTGTGGATGGGAAGACGGTGAGCCAAGTCGACTGGTAGCTTTGTGTACACAAAGTTGTCATCTCTGATGACCCAGGCAATGAAGTCACG[G/T]
ACTAGATTGTGCACTCTGCAGCTGTTTACCTTGCCTGAATTTCCAACATCACCAGGAAGAACAAATCTTTGAGCGAGAAGAGCATCAAAACATCGGTTGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.20% 2.70% 0.49% 2.54% NA
All Indica  2759 94.70% 4.60% 0.65% 0.04% NA
All Japonica  1512 92.10% 0.10% 0.26% 7.61% NA
Aus  269 98.50% 0.00% 0.37% 1.12% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 81.10% 16.10% 2.80% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 93.00% 6.20% 0.64% 0.13% NA
Temperate Japonica  767 99.30% 0.00% 0.26% 0.39% NA
Tropical Japonica  504 86.90% 0.20% 0.40% 12.50% NA
Japonica Intermediate  241 79.70% 0.00% 0.00% 20.33% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126219428 C -> A LOC_Os11g43420.1 synonymous_variant ; p.Val533Val; LOW synonymous_codon Average:45.959; most accessible tissue: Callus, score: 75.956 N N N N
vg1126219428 C -> DEL LOC_Os11g43420.1 N frameshift_variant Average:45.959; most accessible tissue: Callus, score: 75.956 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126219428 8.14E-08 4.41E-09 mr1238 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
vg1126219428 NA 1.00E-06 mr1309 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
vg1126219428 8.89E-06 1.81E-06 mr1484 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
vg1126219428 1.56E-06 2.69E-07 mr1841 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
vg1126219428 9.78E-07 3.56E-08 mr1238_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
vg1126219428 2.54E-06 8.03E-08 mr1484_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
vg1126219428 1.16E-06 8.20E-08 mr1841_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
vg1126219428 NA 4.43E-06 mr1900_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