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Detailed information for vg1121697590:

Variant ID: vg1121697590 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21697590
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTAAAACTTTTATTTTGGTCATTTCTTCATACGACAAAGTGATAGTAACATTATTCATAAAATTGACATATCTCTTATCTGGTTTTATAAACTATAACA[C/A]
ATATATGTAAAATTTATGAATAATATTACTAACATTTCGTTGGATGAAGAAATAACAAAAATAAAAGTTTTAGATCTTGATGAATTATTCAACTTTGTTG

Reverse complement sequence

CAACAAAGTTGAATAATTCATCAAGATCTAAAACTTTTATTTTTGTTATTTCTTCATCCAACGAAATGTTAGTAATATTATTCATAAATTTTACATATAT[G/T]
TGTTATAGTTTATAAAACCAGATAAGAGATATGTCAATTTTATGAATAATGTTACTATCACTTTGTCGTATGAAGAAATGACCAAAATAAAAGTTTTAGA

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 92.90% 4.70% 2.48% 0.00% NA
All Indica  2759 92.80% 4.30% 2.86% 0.00% NA
All Japonica  1512 98.30% 1.20% 0.53% 0.00% NA
Aus  269 59.50% 29.70% 10.78% 0.00% NA
Indica I  595 70.30% 17.80% 11.93% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.20% 0.70% 0.11% 0.00% NA
Indica Intermediate  786 98.10% 1.00% 0.89% 0.00% NA
Temperate Japonica  767 96.70% 2.20% 1.04% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 1.11% 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
vg1121697590 C -> A LOC_Os11g36740-LOC_Os11g36760 intergenic_region ; MODIFIER silent_mutation Average:10.969; most accessible tissue: Zhenshan97 flag leaf, score: 20.297 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121697590 NA 7.31E-06 mr1042_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
vg1121697590 NA 3.44E-06 mr1291_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
vg1121697590 NA 2.55E-06 mr1479_2 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
vg1121697590 NA 4.68E-07 mr1502_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
vg1121697590 NA 3.02E-06 mr1742_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