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Detailed information for vg0418137389:

Variant ID: vg0418137389 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 18137389
Reference Allele: AAlternative Allele: C,AT
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 182. )

Flanking Sequence (100 bp) in Reference Genome:


TAAGAAACATGCCTGGATCAATTTTACCTCCTGTAGAATATTTAGTACGAGCCAAGTTTGGAGGTAATGCAAACACGCATCCCCCTGCACCCCTAAAAAA[A/C,AT]
ATACTAATTAGTGTCAAATGTACCAAAGTAGAAATGATGATAGGTCAGAGCAGAGTGGTAGTGTAGTACATAGTACAATTGTACTACCCTATTTAATGAT

Reverse complement sequence

ATCATTAAATAGGGTAGTACAATTGTACTATGTACTACACTACCACTCTGCTCTGACCTATCATCATTTCTACTTTGGTACATTTGACACTAATTAGTAT[T/G,AT]
TTTTTTAGGGGTGCAGGGGGATGCGTGTTTGCATTACCTCCAAACTTGGCTCGTACTAAATATTCTACAGGAGGTAAAATTGATCCAGGCATGTTTCTTA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.10% 1.00% 0.87% 0.00% NA
All Indica  2759 99.50% 0.20% 0.29% 0.00% NA
All Japonica  1512 95.40% 2.60% 1.98% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 99.00% 0.00% 1.01% 0.00% NA
Indica II  465 98.90% 0.60% 0.43% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 91.40% 5.20% 3.39% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 98.80% 0.00% 1.24% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 96.70% 1.10% 2.22% 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
vg0418137389 A -> C LOC_Os04g30390.1 upstream_gene_variant ; 235.0bp to feature; MODIFIER silent_mutation Average:55.982; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0418137389 A -> C LOC_Os04g30380-LOC_Os04g30390 intergenic_region ; MODIFIER silent_mutation Average:55.982; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0418137389 A -> AT LOC_Os04g30390.1 upstream_gene_variant ; 234.0bp to feature; MODIFIER N Average:55.982; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N
vg0418137389 A -> AT LOC_Os04g30380-LOC_Os04g30390 intergenic_region ; MODIFIER N Average:55.982; most accessible tissue: Zhenshan97 panicle, score: 67.02 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0418137389 7.00E-07 4.50E-08 mr1588_2 Jap_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