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Detailed information for vg0132505947:

Variant ID: vg0132505947 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 32505947
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGACAGGCTTGAGAGGTAGTGGTTTTATTTTGTGGAGGATATCATAACACCAAAATTTGCAAATTTGAAGTCTACGTGTAATTTTGTACTCTGTCACTG[A/G]
AAAATATAAGGCATGCATGTATTTGAAAAGTTGGTAGTTTTAAATTTGAAAGTTCCTTAATATGATGTTAACTTAATAGTCATTGATTATTACAAAAGAA

Reverse complement sequence

TTCTTTTGTAATAATCAATGACTATTAAGTTAACATCATATTAAGGAACTTTCAAATTTAAAACTACCAACTTTTCAAATACATGCATGCCTTATATTTT[T/C]
CAGTGACAGAGTACAAAATTACACGTAGACTTCAAATTTGCAAATTTTGGTGTTATGATATCCTCCACAAAATAAAACCACTACCTCTCAAGCCTGTCCA

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 88.00% 11.90% 0.06% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 71.90% 28.00% 0.07% 0.00% NA
Aus  269 90.30% 9.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 76.70% 23.30% 0.00% 0.00% NA
Tropical Japonica  504 80.20% 19.80% 0.00% 0.00% NA
Japonica Intermediate  241 39.40% 60.20% 0.41% 0.00% NA
VI/Aromatic  96 15.60% 83.30% 1.04% 0.00% NA
Intermediate  90 74.40% 24.40% 1.11% 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
vg0132505947 A -> G LOC_Os01g56380.1 upstream_gene_variant ; 2990.0bp to feature; MODIFIER silent_mutation Average:33.884; most accessible tissue: Callus, score: 70.323 N N N N
vg0132505947 A -> G LOC_Os01g56390.1 downstream_gene_variant ; 2449.0bp to feature; MODIFIER silent_mutation Average:33.884; most accessible tissue: Callus, score: 70.323 N N N N
vg0132505947 A -> G LOC_Os01g56380-LOC_Os01g56390 intergenic_region ; MODIFIER silent_mutation Average:33.884; most accessible tissue: Callus, score: 70.323 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0132505947 NA 2.68E-06 mr1149 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
vg0132505947 NA 3.72E-06 mr1180 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
vg0132505947 NA 1.31E-07 mr1183 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
vg0132505947 NA 2.80E-12 mr1205 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
vg0132505947 NA 4.52E-06 mr1293 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
vg0132505947 NA 1.39E-06 mr1315 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
vg0132505947 NA 3.82E-06 mr1418 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
vg0132505947 NA 2.52E-07 mr1503 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
vg0132505947 NA 1.14E-08 mr1506 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
vg0132505947 4.80E-06 4.80E-06 mr1506 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
vg0132505947 NA 1.82E-08 mr1776 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
vg0132505947 NA 4.51E-10 mr1947_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