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Detailed information for vg1122934110:

Variant ID: vg1122934110 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22934110
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTTTACTCGTGACTTATGTTTTTAATTTCTTTCAAAAAAATTTCAAATAAGACGGACGGTCAAAGTTAGGCGCGAAAAACCATGACTACACTTAAAAT[G/A]
GGACGGAGGGAGTATTAGGTTTATCTTTTACAGAATGGAGGGAGTACTTCATTCATTCGAAAGCACTCTCTGCTATTATCTATTCATTAAAAAAATGAGG

Reverse complement sequence

CCTCATTTTTTTAATGAATAGATAATAGCAGAGAGTGCTTTCGAATGAATGAAGTACTCCCTCCATTCTGTAAAAGATAAACCTAATACTCCCTCCGTCC[C/T]
ATTTTAAGTGTAGTCATGGTTTTTCGCGCCTAACTTTGACCGTCCGTCTTATTTGAAATTTTTTTGAAAGAAATTAAAAACATAAGTCACGAGTAAAGTA

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 95.00% 4.80% 0.23% 0.00% NA
All Indica  2759 99.50% 0.40% 0.04% 0.00% NA
All Japonica  1512 85.30% 14.10% 0.66% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.50% 0.40% 0.11% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 90.00% 9.90% 0.13% 0.00% NA
Tropical Japonica  504 80.40% 19.60% 0.00% 0.00% NA
Japonica Intermediate  241 80.50% 15.80% 3.73% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1122934110 G -> A LOC_Os11g38650-LOC_Os11g38660 intergenic_region ; MODIFIER silent_mutation Average:35.04; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122934110 4.61E-06 NA mr1049_2 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
vg1122934110 4.14E-06 NA mr1136_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
vg1122934110 5.20E-06 5.20E-06 mr1547_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
vg1122934110 NA 2.45E-06 mr1559_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
vg1122934110 9.22E-06 9.22E-06 mr1610_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
vg1122934110 3.76E-06 NA mr1676_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
vg1122934110 NA 2.36E-07 mr1676_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
vg1122934110 9.75E-06 NA mr1980_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