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Detailed information for vg0124418602:

Variant ID: vg0124418602 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24418602
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAACTCCAAAATGAAAATGATTAATTAGATTTATGCCACTGTAAATATTGAGGTTTTAAAATATACCATTATAATTTACGTATTTGTAACAATGCCACG[A/G]
TCACTTGTTTATAATTTCAGTTGTACCATTAAGATATGTATTTTACCTGTATTTGATAAAAATGTCCTCACCCTCTGGTGGTCGAGCGGGACAGGTGGAC

Reverse complement sequence

GTCCACCTGTCCCGCTCGACCACCAGAGGGTGAGGACATTTTTATCAAATACAGGTAAAATACATATCTTAATGGTACAACTGAAATTATAAACAAGTGA[T/C]
CGTGGCATTGTTACAAATACGTAAATTATAATGGTATATTTTAAAACCTCAATATTTACAGTGGCATAAATCTAATTAATCATTTTCATTTTGGAGTTGA

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 75.00% 24.80% 0.21% 0.00% NA
All Indica  2759 99.60% 0.30% 0.11% 0.00% NA
All Japonica  1512 30.20% 69.40% 0.40% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 99.10% 0.60% 0.25% 0.00% NA
Temperate Japonica  767 1.70% 98.20% 0.13% 0.00% NA
Tropical Japonica  504 67.30% 32.10% 0.60% 0.00% NA
Japonica Intermediate  241 43.20% 56.00% 0.83% 0.00% NA
VI/Aromatic  96 13.50% 86.50% 0.00% 0.00% NA
Intermediate  90 66.70% 32.20% 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
vg0124418602 A -> G LOC_Os01g42909.1 upstream_gene_variant ; 1754.0bp to feature; MODIFIER silent_mutation Average:56.406; most accessible tissue: Callus, score: 81.33 N N N N
vg0124418602 A -> G LOC_Os01g42920.1 downstream_gene_variant ; 1881.0bp to feature; MODIFIER silent_mutation Average:56.406; most accessible tissue: Callus, score: 81.33 N N N N
vg0124418602 A -> G LOC_Os01g42909-LOC_Os01g42920 intergenic_region ; MODIFIER silent_mutation Average:56.406; most accessible tissue: Callus, score: 81.33 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124418602 NA 7.32E-07 mr1518 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
vg0124418602 NA 4.56E-45 mr1563 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
vg0124418602 6.29E-06 NA mr1676 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
vg0124418602 NA 3.74E-08 mr1676 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
vg0124418602 NA 8.64E-18 mr1156_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
vg0124418602 2.96E-07 NA mr1676_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
vg0124418602 2.09E-06 2.01E-08 mr1676_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
vg0124418602 NA 3.24E-06 mr1840_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