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Detailed information for vg1125224256:

Variant ID: vg1125224256 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25224256
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTGCTTCCTGCTCCCACCTCATCGCCTCAGGATGCAGCTAGTTTAGGCTGTGCTTAGTTCCTCGGTCAAAAATTTTTTAAGTACACAAACACACATTT[G/A]
AAATATTAAACGTAGACTAATAACAAAACAAATTATAGATTCCGTATGTAAACTGCGAGATGAATTTATTAAGTCTAATTAATTTATCATTAGCGAATGT

Reverse complement sequence

ACATTCGCTAATGATAAATTAATTAGACTTAATAAATTCATCTCGCAGTTTACATACGGAATCTATAATTTGTTTTGTTATTAGTCTACGTTTAATATTT[C/T]
AAATGTGTGTTTGTGTACTTAAAAAATTTTTGACCGAGGAACTAAGCACAGCCTAAACTAGCTGCATCCTGAGGCGATGAGGTGGGAGCAGGAAGCACAT

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 68.00% 31.70% 0.25% 0.00% NA
All Indica  2759 54.90% 44.80% 0.33% 0.00% NA
All Japonica  1512 87.40% 12.50% 0.13% 0.00% NA
Aus  269 79.90% 19.70% 0.37% 0.00% NA
Indica I  595 40.30% 58.80% 0.84% 0.00% NA
Indica II  465 93.80% 6.00% 0.22% 0.00% NA
Indica III  913 44.50% 55.40% 0.11% 0.00% NA
Indica Intermediate  786 55.00% 44.80% 0.25% 0.00% NA
Temperate Japonica  767 97.70% 2.20% 0.13% 0.00% NA
Tropical Japonica  504 71.80% 28.20% 0.00% 0.00% NA
Japonica Intermediate  241 87.10% 12.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg1125224256 G -> A LOC_Os11g41940.1 upstream_gene_variant ; 1412.0bp to feature; MODIFIER silent_mutation Average:45.416; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg1125224256 G -> A LOC_Os11g41920.1 downstream_gene_variant ; 1899.0bp to feature; MODIFIER silent_mutation Average:45.416; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N
vg1125224256 G -> A LOC_Os11g41920-LOC_Os11g41940 intergenic_region ; MODIFIER silent_mutation Average:45.416; most accessible tissue: Zhenshan97 panicle, score: 65.386 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125224256 NA 3.14E-06 mr1159 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
vg1125224256 1.09E-09 NA mr1191 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
vg1125224256 1.18E-08 1.26E-07 mr1191 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
vg1125224256 NA 1.65E-06 mr1441 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
vg1125224256 NA 3.02E-07 mr1583 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
vg1125224256 9.97E-11 NA mr1644 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
vg1125224256 7.43E-10 4.65E-08 mr1644 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
vg1125224256 4.40E-06 NA 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
vg1125224256 1.15E-07 3.28E-08 mr1794 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
vg1125224256 NA 8.74E-06 mr1150_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
vg1125224256 NA 3.01E-06 mr1159_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
vg1125224256 2.55E-10 NA mr1191_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
vg1125224256 7.89E-09 2.05E-08 mr1191_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
vg1125224256 NA 5.41E-07 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
vg1125224256 NA 2.61E-08 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
vg1125224256 NA 6.92E-06 mr1895_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
vg1125224256 NA 6.48E-08 mr1933_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