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Detailed information for vg0418036086:

Variant ID: vg0418036086 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 18036086
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCACGTCAATGCCACGTGGGACGAAGACCAAGTACGTTAACACTGCCACGTGTGCGCCACGTCAACAAAACCACTAAGGGAGTCAAATTGTACCGGTTTT[G/A]
TAAGTTGAGGGTTTAAGATTTCTGGTATTGTGGTTGAGGGATACGATTTAGATTCGGTGGTCAGTTGAGAGAGTCAAAGTGATCTTATTCCTTTCTCACT

Reverse complement sequence

AGTGAGAAAGGAATAAGATCACTTTGACTCTCTCAACTGACCACCGAATCTAAATCGTATCCCTCAACCACAATACCAGAAATCTTAAACCCTCAACTTA[C/T]
AAAACCGGTACAATTTGACTCCCTTAGTGGTTTTGTTGACGTGGCGCACACGTGGCAGTGTTAACGTACTTGGTCTTCGTCCCACGTGGCATTGACGTGA

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 97.90% 1.20% 0.91% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 93.70% 3.50% 2.78% 0.00% 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 99.80% 0.00% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.80% 1.60% 0.65% 0.00% NA
Tropical Japonica  504 90.70% 4.00% 5.36% 0.00% NA
Japonica Intermediate  241 87.10% 8.70% 4.15% 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
vg0418036086 G -> A LOC_Os04g30230.1 upstream_gene_variant ; 1732.0bp to feature; MODIFIER silent_mutation Average:63.191; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg0418036086 G -> A LOC_Os04g30220.1 downstream_gene_variant ; 3632.0bp to feature; MODIFIER silent_mutation Average:63.191; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N
vg0418036086 G -> A LOC_Os04g30220-LOC_Os04g30230 intergenic_region ; MODIFIER silent_mutation Average:63.191; most accessible tissue: Zhenshan97 panicle, score: 80.486 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0418036086 7.77E-06 6.29E-09 mr1104 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
vg0418036086 NA 5.72E-06 mr1139 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
vg0418036086 NA 5.84E-07 mr1155 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
vg0418036086 NA 2.02E-09 mr1213 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
vg0418036086 NA 1.13E-06 mr1224 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
vg0418036086 NA 2.24E-06 mr1225 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
vg0418036086 NA 4.24E-06 mr1246 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
vg0418036086 NA 5.86E-06 mr1411 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
vg0418036086 9.05E-06 9.15E-08 mr1437 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
vg0418036086 NA 4.26E-06 mr1620 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
vg0418036086 7.97E-06 NA mr1104_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
vg0418036086 NA 2.59E-06 mr1224_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
vg0418036086 NA 8.02E-06 mr1246_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