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Detailed information for vg0416940273:

Variant ID: vg0416940273 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16940273
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTCATCGGAAATTCATTGAAATTTAGAGGGAAAATATCATTATGATAGAGTTAAGAGGAAATATGAAGAGACATGGAGCATTGGACTTATCGAAGGACAT[C/A]
TGTCGAAACAATATTTCAGCAATATAAAGAGGGTAGCCACGAAACCTAAAAGTGGATGGATGCGGAGATAAAGGATTTACACAGGTTCAGGCCCTCTCAA

Reverse complement sequence

TTGAGAGGGCCTGAACCTGTGTAAATCCTTTATCTCCGCATCCATCCACTTTTAGGTTTCGTGGCTACCCTCTTTATATTGCTGAAATATTGTTTCGACA[G/T]
ATGTCCTTCGATAAGTCCAATGCTCCATGTCTCTTCATATTTCCTCTTAACTCTATCATAATGATATTTTCCCTCTAAATTTCAATGAATTTCCGATGAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.30% 1.60% 0.80% 0.28% NA
All Indica  2759 96.00% 2.60% 1.27% 0.04% NA
All Japonica  1512 99.90% 0.00% 0.13% 0.00% NA
Aus  269 95.20% 0.00% 0.37% 4.46% NA
Indica I  595 88.70% 8.60% 2.69% 0.00% NA
Indica II  465 97.80% 1.10% 1.08% 0.00% NA
Indica III  913 99.80% 0.00% 0.11% 0.11% NA
Indica Intermediate  786 96.20% 2.20% 1.65% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0416940273 C -> DEL N N silent_mutation Average:40.719; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N
vg0416940273 C -> A LOC_Os04g28620.1 upstream_gene_variant ; 4932.0bp to feature; MODIFIER silent_mutation Average:40.719; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N
vg0416940273 C -> A LOC_Os04g28600-LOC_Os04g28620 intergenic_region ; MODIFIER silent_mutation Average:40.719; most accessible tissue: Zhenshan97 young leaf, score: 60.8 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416940273 NA 5.75E-06 mr1746 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
vg0416940273 3.72E-07 3.27E-08 mr1746_2 Ind_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