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Detailed information for vg1122247251:

Variant ID: vg1122247251 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22247251
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGGGAGTAATACTAACACTTGGACCGATAATACTTGTCGTTTTAGAAAAAATGTGAGGTCAATGTTTAGAATAATTTTATAAATTATTTTTAAAATATTT[G/A]
TCTTTTTAAATATGGTGAGTACATATATAAATTAGTCTTAAAAAGTATTTTAATAAAATCATATATTCGTTAACATTTTTATACATATTATAATGAAAAA

Reverse complement sequence

TTTTTCATTATAATATGTATAAAAATGTTAACGAATATATGATTTTATTAAAATACTTTTTAAGACTAATTTATATATGTACTCACCATATTTAAAAAGA[C/T]
AAATATTTTAAAAATAATTTATAAAATTATTCTAAACATTGACCTCACATTTTTTCTAAAACGACAAGTATTATCGGTCCAAGTGTTAGTATTACTCCCT

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 93.30% 6.60% 0.15% 0.00% NA
All Indica  2759 90.50% 9.40% 0.11% 0.00% NA
All Japonica  1512 98.10% 1.70% 0.20% 0.00% NA
Aus  269 91.80% 7.80% 0.37% 0.00% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 85.20% 14.50% 0.33% 0.00% NA
Indica Intermediate  786 88.80% 11.20% 0.00% 0.00% NA
Temperate Japonica  767 97.00% 3.00% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 0.40% 0.60% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1122247251 G -> A LOC_Os11g37670.1 upstream_gene_variant ; 2821.0bp to feature; MODIFIER silent_mutation Average:43.473; most accessible tissue: Callus, score: 68.56 N N N N
vg1122247251 G -> A LOC_Os11g37670-LOC_Os11g37680 intergenic_region ; MODIFIER silent_mutation Average:43.473; most accessible tissue: Callus, score: 68.56 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1122247251 4.48E-06 4.49E-06 mr1160 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
vg1122247251 2.51E-06 2.51E-06 mr1160 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
vg1122247251 NA 1.96E-09 mr1798 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
vg1122247251 NA 4.03E-11 mr1798_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