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Detailed information for vg1114197693:

Variant ID: vg1114197693 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 14197693
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


ATCAGAAGGATCTAGGGGAATCTTCTTAGTCTTGGCTTCGCTTTCTCCGCTCTTCGAGACCTTGGTTGCGGGCACCTCTCCTTCGCTTGCTGTGGACGCA[G/A]
CCAGTCGGACATCTTCCCGGGCGGACGCCATCTCGCGAGTTTGGGCCATCTCGCAACTTTCCTTGTCGCATGTGACGGCTTGCTTGATGTCGCTCCATAG

Reverse complement sequence

CTATGGAGCGACATCAAGCAAGCCGTCACATGCGACAAGGAAAGTTGCGAGATGGCCCAAACTCGCGAGATGGCGTCCGCCCGGGAAGATGTCCGACTGG[C/T]
TGCGTCCACAGCAAGCGAAGGAGAGGTGCCCGCAACCAAGGTCTCGAAGAGCGGAGAAAGCGAAGCCAAGACTAAGAAGATTCCCCTAGATCCTTCTGAT

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 94.40% 3.00% 2.31% 0.32% NA
All Indica  2759 99.60% 0.10% 0.36% 0.00% NA
All Japonica  1512 83.30% 9.20% 6.55% 0.99% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.20% 0.20% 0.67% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.10% 0.76% 0.00% NA
Temperate Japonica  767 75.70% 13.20% 9.52% 1.56% NA
Tropical Japonica  504 96.00% 2.00% 1.98% 0.00% NA
Japonica Intermediate  241 80.50% 11.60% 6.64% 1.24% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1114197693 G -> A LOC_Os11g24930.1 missense_variant ; p.Ala811Val; MODERATE nonsynonymous_codon ; A811V Average:51.505; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 benign 1.164 DELETERIOUS 0.02
vg1114197693 G -> DEL LOC_Os11g24930.1 N frameshift_variant Average:51.505; most accessible tissue: Zhenshan97 flag leaf, score: 64.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1114197693 1.09E-07 NA mr1137 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
vg1114197693 6.51E-06 5.38E-08 mr1424 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
vg1114197693 1.99E-07 NA mr1617 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