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Detailed information for vg1126180021:

Variant ID: vg1126180021 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26180021
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, C: 0.41, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


AAGGCATGGACATGTTGTTTATGAATTTCTGGACTGAAGCATCCAGAACGCAGTGTTTACACCCAAATTTGGCACTTAGGATTAAAATAGGAAATATTGC[T/C]
AAAATTTGGAAGTCTACCGGTTTCCTCCGAGGTAGGCCGGTCTGACCGCCGTGTGTTGGGCGGTCAGACCGCCGGTTGAGGGCCGGTCAGACCGGCGGTG

Reverse complement sequence

CACCGCCGGTCTGACCGGCCCTCAACCGGCGGTCTGACCGCCCAACACACGGCGGTCAGACCGGCCTACCTCGGAGGAAACCGGTAGACTTCCAAATTTT[A/G]
GCAATATTTCCTATTTTAATCCTAAGTGCCAAATTTGGGTGTAAACACTGCGTTCTGGATGCTTCAGTCCAGAAATTCATAAACAACATGTCCATGCCTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 30.00% 25.80% 1.25% 42.98% NA
All Indica  2759 13.80% 27.10% 1.67% 57.41% NA
All Japonica  1512 65.30% 20.00% 0.33% 14.35% NA
Aus  269 2.20% 42.00% 1.49% 54.28% NA
Indica I  595 7.90% 21.30% 1.85% 68.91% NA
Indica II  465 7.50% 62.40% 2.15% 27.96% NA
Indica III  913 22.30% 8.00% 1.20% 68.46% NA
Indica Intermediate  786 12.00% 33.00% 1.78% 53.31% NA
Temperate Japonica  767 64.40% 32.50% 0.39% 2.74% NA
Tropical Japonica  504 71.40% 3.40% 0.40% 24.80% NA
Japonica Intermediate  241 55.20% 15.40% 0.00% 29.46% NA
VI/Aromatic  96 18.80% 31.20% 2.08% 47.92% NA
Intermediate  90 30.00% 25.60% 2.22% 42.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126180021 T -> DEL N N silent_mutation Average:47.165; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg1126180021 T -> C LOC_Os11g43370.1 upstream_gene_variant ; 1405.0bp to feature; MODIFIER silent_mutation Average:47.165; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg1126180021 T -> C LOC_Os11g43360-LOC_Os11g43370 intergenic_region ; MODIFIER silent_mutation Average:47.165; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126180021 6.76E-06 9.35E-08 mr1668 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
vg1126180021 NA 8.29E-06 mr1060_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
vg1126180021 NA 9.69E-06 mr1358_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
vg1126180021 NA 1.39E-06 mr1576_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