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Detailed information for vg1125536503:

Variant ID: vg1125536503 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25536503
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CAGCAGTTGCAGGTTAGTGTTATATTCTTTTTATTTGGTCAATATAAATTACTTGTGAACTTCTTAATGTCAACAGCAATATTTTGTAATTAATTCAGGA[A/G]
TTCCTGCTTTTTGAGAGAGAATGCTACCTATCTAAAATGGAGCTTGAGGAAGAGCAGTTAGAGCAGTTACCTGCTGATGGCTAAAAGGTTGATGTTACAT

Reverse complement sequence

ATGTAACATCAACCTTTTAGCCATCAGCAGGTAACTGCTCTAACTGCTCTTCCTCAAGCTCCATTTTAGATAGGTAGCATTCTCTCTCAAAAAGCAGGAA[T/C]
TCCTGAATTAATTACAAAATATTGCTGTTGACATTAAGAAGTTCACAAGTAATTTATATTGACCAAATAAAAAGAATATAACACTAACCTGCAACTGCTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.30% 9.70% 0.00% 0.00% NA
All Indica  2759 92.60% 7.40% 0.00% 0.00% NA
All Japonica  1512 88.50% 11.50% 0.00% 0.00% NA
Aus  269 73.20% 26.80% 0.00% 0.00% NA
Indica I  595 97.50% 2.50% 0.00% 0.00% NA
Indica II  465 97.40% 2.60% 0.00% 0.00% NA
Indica III  913 83.20% 16.80% 0.00% 0.00% NA
Indica Intermediate  786 96.80% 3.20% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 72.00% 28.00% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg1125536503 A -> G LOC_Os11g42420.1 splice_region_variant&synonymous_variant ; p.Glu1061Glu; LOW synonymous_codon Average:49.992; most accessible tissue: Callus, score: 80.546 N N N N
vg1125536503 A -> G LOC_Os11g42420.2 splice_region_variant&synonymous_variant ; p.Glu1061Glu; LOW synonymous_codon Average:49.992; most accessible tissue: Callus, score: 80.546 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125536503 NA 9.64E-07 mr1543 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
vg1125536503 4.22E-06 NA mr1662 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
vg1125536503 1.47E-06 1.13E-07 mr1662 Jap_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
vg1125536503 4.00E-06 NA mr1238_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
vg1125536503 1.90E-06 1.91E-08 mr1662_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
vg1125536503 2.25E-06 1.37E-06 mr1662_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
vg1125536503 3.56E-06 NA mr1841_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
vg1125536503 4.14E-06 NA mr1900_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