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Detailed information for vg0416033751:

Variant ID: vg0416033751 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16033751
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATATATACCGATCATAAGAGTTTGAAATACATCTTCACTCAGTCGGATCTGAATCTTCGGCAGAGAAGATGGTTAGAACTCATCAAGGATTATGATGTG[A/G]
GAATTCACTATCATCCTGGCAAGGCCAACGTGGTCGCCGACCCTCTAAGTCGAAAAAGCCATTGCAACACTCTTGGCGTCCGTGGCATTCCACCGGAACT

Reverse complement sequence

AGTTCCGGTGGAATGCCACGGACGCCAAGAGTGTTGCAATGGCTTTTTCGACTTAGAGGGTCGGCGACCACGTTGGCCTTGCCAGGATGATAGTGAATTC[T/C]
CACATCATAATCCTTGATGAGTTCTAACCATCTTCTCTGCCGAAGATTCAGATCCGACTGAGTGAAGATGTATTTCAAACTCTTATGATCGGTATATATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.20% 3.50% 12.89% 3.41% NA
All Indica  2759 77.00% 5.80% 11.96% 5.26% NA
All Japonica  1512 99.50% 0.40% 0.13% 0.00% NA
Aus  269 9.70% 0.40% 89.22% 0.74% NA
Indica I  595 89.10% 10.80% 0.00% 0.17% NA
Indica II  465 81.30% 0.90% 13.98% 3.87% NA
Indica III  913 62.30% 7.00% 20.37% 10.30% NA
Indica Intermediate  786 82.40% 3.40% 10.05% 4.07% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 57.30% 1.00% 29.17% 12.50% NA
Intermediate  90 87.80% 0.00% 10.00% 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
vg0416033751 A -> DEL N N silent_mutation Average:53.691; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0416033751 A -> G LOC_Os04g27092.1 upstream_gene_variant ; 1541.0bp to feature; MODIFIER silent_mutation Average:53.691; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N
vg0416033751 A -> G LOC_Os04g27092-LOC_Os04g27094 intergenic_region ; MODIFIER silent_mutation Average:53.691; most accessible tissue: Minghui63 young leaf, score: 81.5 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416033751 1.49E-06 2.80E-08 mr1043_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
vg0416033751 1.56E-06 6.42E-08 mr1185_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
vg0416033751 NA 1.21E-06 mr1269_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
vg0416033751 NA 5.50E-07 mr1479_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
vg0416033751 7.37E-06 3.12E-07 mr1677_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
vg0416033751 9.14E-07 4.05E-06 mr1912_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