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Detailed information for vg1125229010:

Variant ID: vg1125229010 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25229010
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCTGGATACAAGAACTTCTCCGAGGAATTACTTGCATGTTTCCTCGTCGATCGGCTGGATGACTACTTCGCTAGAAAGAACAAGATACATGACAAGCGC[G/A]
TGAAACCAATCCTGGAGTTGGTAAAAAAAACCAATCCTGGAGTTGGTAAAAAAAACCAATCCTGGAGTTGGTAAAAAAAACCAATCCTGGAGGAGCAGAG

Reverse complement sequence

CTCTGCTCCTCCAGGATTGGTTTTTTTTACCAACTCCAGGATTGGTTTTTTTTACCAACTCCAGGATTGGTTTTTTTTACCAACTCCAGGATTGGTTTCA[C/T]
GCGCTTGTCATGTATCTTGTTCTTTCTAGCGAAGTAGTCATCCAGCCGATCGACGAGGAAACATGCAAGTAATTCCTCGGAGAAGTTCTTGTATCCAGGT

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 94.60% 2.80% 1.48% 1.12% NA
All Indica  2759 99.90% 0.00% 0.00% 0.07% NA
All Japonica  1512 83.90% 8.30% 4.50% 3.24% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.00% 0.00% 0.43% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 73.00% 13.70% 8.21% 5.08% NA
Tropical Japonica  504 98.20% 1.40% 0.20% 0.20% NA
Japonica Intermediate  241 88.80% 5.80% 1.66% 3.73% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 4.40% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125229010 G -> A LOC_Os11g41960.1 upstream_gene_variant ; 3282.0bp to feature; MODIFIER silent_mutation Average:51.968; most accessible tissue: Callus, score: 77.93 N N N N
vg1125229010 G -> A LOC_Os11g41940.1 downstream_gene_variant ; 1684.0bp to feature; MODIFIER silent_mutation Average:51.968; most accessible tissue: Callus, score: 77.93 N N N N
vg1125229010 G -> A LOC_Os11g41950.1 downstream_gene_variant ; 1359.0bp to feature; MODIFIER silent_mutation Average:51.968; most accessible tissue: Callus, score: 77.93 N N N N
vg1125229010 G -> A LOC_Os11g41940-LOC_Os11g41950 intergenic_region ; MODIFIER silent_mutation Average:51.968; most accessible tissue: Callus, score: 77.93 N N N N
vg1125229010 G -> DEL N N silent_mutation Average:51.968; most accessible tissue: Callus, score: 77.93 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125229010 2.72E-07 NA mr1238 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
vg1125229010 2.90E-07 NA mr1309 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
vg1125229010 4.54E-10 NA mr1484 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
vg1125229010 4.85E-07 NA mr1484 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
vg1125229010 1.20E-06 9.97E-10 mr1530 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
vg1125229010 NA 1.08E-06 mr1530 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
vg1125229010 NA 7.84E-06 mr1826 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
vg1125229010 1.02E-06 NA mr1841 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
vg1125229010 6.56E-06 NA mr1900 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
vg1125229010 5.70E-09 NA mr1238_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
vg1125229010 3.08E-11 NA mr1484_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
vg1125229010 1.44E-08 NA mr1530_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
vg1125229010 NA 1.30E-11 mr1530_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
vg1125229010 7.28E-09 NA mr1841_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
vg1125229010 2.89E-08 NA mr1900_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
vg1125229010 6.34E-10 NA mr1945_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