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Detailed information for vg1125171777:

Variant ID: vg1125171777 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25171777
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


TAACTATCCATTTTTGTTTTCAGCCACCAACGAATAACAACAATGGATGTCCTCCTCCTGCCGCCGTTGCCGGCGCCGGAGACGACGGCGCCGGCGGGGA[G/T]
GGACTGGTCGGAGCTGCCGGCGGACGTGCTGTCGGTGGTGTTCGCCAAGGTGGGCGCCGTCGAGGTCCTCGCCGGCGCGGGCCTCGCGTGCCGCTCGTGG

Reverse complement sequence

CCACGAGCGGCACGCGAGGCCCGCGCCGGCGAGGACCTCGACGGCGCCCACCTTGGCGAACACCACCGACAGCACGTCCGCCGGCAGCTCCGACCAGTCC[C/A]
TCCCCGCCGGCGCCGTCGTCTCCGGCGCCGGCAACGGCGGCAGGAGGAGGACATCCATTGTTGTTATTCGTTGGTGGCTGAAAACAAAAATGGATAGTTA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.40% 8.60% 0.02% 0.00% NA
All Indica  2759 89.20% 10.80% 0.04% 0.00% NA
All Japonica  1512 93.40% 6.60% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 84.10% 15.90% 0.00% 0.00% NA
Indica III  913 85.70% 14.30% 0.00% 0.00% NA
Indica Intermediate  786 88.70% 11.20% 0.13% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 82.50% 17.50% 0.00% 0.00% NA
Japonica Intermediate  241 95.40% 4.60% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg1125171777 G -> T LOC_Os11g41860.1 missense_variant ; p.Arg20Met; MODERATE nonsynonymous_codon ; R20M Average:75.12; most accessible tissue: Callus, score: 92.228 unknown unknown DELETERIOUS 0.02
vg1125171777 G -> T LOC_Os11g41860.2 missense_variant ; p.Arg20Met; MODERATE nonsynonymous_codon ; R20M Average:75.12; most accessible tissue: Callus, score: 92.228 unknown unknown DELETERIOUS 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125171777 NA 3.16E-06 mr1543 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
vg1125171777 NA 1.14E-08 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
vg1125171777 2.61E-06 4.33E-06 mr1808 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
vg1125171777 NA 1.75E-07 mr1892 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
vg1125171777 NA 9.76E-06 mr1892 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
vg1125171777 5.94E-07 NA mr1133_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
vg1125171777 NA 6.50E-06 mr1218_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
vg1125171777 NA 1.08E-06 mr1850_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