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Detailed information for vg1125520282:

Variant ID: vg1125520282 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25520282
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTACCACTTATGCCCGTCACAGATATGTCGTCACAGGTGTGAGGATCTGGTGTAGTGAATATGTGTTTAAACATCACTGCAGAAAAAGAAAAATGCATGT[T/C]
GTTGATTTCGGAGTGACGGTGCTGCTTCATTTTCCTCTCCATGAGAGCGATCGCCGTGCTCAAACTATAGCTAGAGCTAGCAGCCCTTTTATTTGTTTTG

Reverse complement sequence

CAAAACAAATAAAAGGGCTGCTAGCTCTAGCTATAGTTTGAGCACGGCGATCGCTCTCATGGAGAGGAAAATGAAGCAGCACCGTCACTCCGAAATCAAC[A/G]
ACATGCATTTTTCTTTTTCTGCAGTGATGTTTAAACACATATTCACTACACCAGATCCTCACACCTGTGACGACATATCTGTGACGGGCATAAGTGGTAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.10% 10.80% 0.02% 0.00% NA
All Indica  2759 82.10% 17.90% 0.04% 0.00% NA
All Japonica  1512 98.90% 1.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.80% 5.20% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 69.20% 30.70% 0.11% 0.00% NA
Indica Intermediate  786 77.50% 22.50% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg1125520282 T -> C LOC_Os11g42390.1 downstream_gene_variant ; 4564.0bp to feature; MODIFIER silent_mutation Average:48.406; most accessible tissue: Zhenshan97 root, score: 74.04 N N N N
vg1125520282 T -> C LOC_Os11g42400.1 downstream_gene_variant ; 373.0bp to feature; MODIFIER silent_mutation Average:48.406; most accessible tissue: Zhenshan97 root, score: 74.04 N N N N
vg1125520282 T -> C LOC_Os11g42410.1 downstream_gene_variant ; 2365.0bp to feature; MODIFIER silent_mutation Average:48.406; most accessible tissue: Zhenshan97 root, score: 74.04 N N N N
vg1125520282 T -> C LOC_Os11g42400-LOC_Os11g42410 intergenic_region ; MODIFIER silent_mutation Average:48.406; most accessible tissue: Zhenshan97 root, score: 74.04 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125520282 NA 1.50E-08 mr1133 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
vg1125520282 NA 5.85E-06 mr1533 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
vg1125520282 NA 1.28E-06 mr1667 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
vg1125520282 1.01E-06 2.73E-15 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
vg1125520282 5.41E-06 5.24E-11 mr1133_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
vg1125520282 7.62E-06 4.10E-09 mr1667_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