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Detailed information for vg0127041496:

Variant ID: vg0127041496 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 27041496
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAAATTGGGTCTCATACAAGACACAGCTTCAACACGAGAACCTATGCAGTAGACACTATCAAGTTTTGCATTGGGGGAGAATAGTTTCTTCATAATAGAT[A/G]
AAGAATAAATATGATTGGTAGAGAAGAGAGATGATGTATTTATTAATGGTCCACTTTAAGAAACCATAAGTTATGGAGTGTAATTTTTATTGTGATGTCT

Reverse complement sequence

AGACATCACAATAAAAATTACACTCCATAACTTATGGTTTCTTAAAGTGGACCATTAATAAATACATCATCTCTCTTCTCTACCAATCATATTTATTCTT[T/C]
ATCTATTATGAAGAAACTATTCTCCCCCAATGCAAAACTTGATAGTGTCTACTGCATAGGTTCTCGTGTTGAAGCTGTGTCTTGTATGAGACCCAATTTC

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 68.60% 31.40% 0.00% 0.00% NA
All Indica  2759 99.10% 0.90% 0.00% 0.00% NA
All Japonica  1512 15.50% 84.50% 0.00% 0.00% NA
Aus  269 80.30% 19.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 41.70% 58.30% 0.00% 0.00% NA
Japonica Intermediate  241 8.30% 91.70% 0.00% 0.00% NA
VI/Aromatic  96 8.30% 91.70% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 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
vg0127041496 A -> G LOC_Os01g47330.1 upstream_gene_variant ; 295.0bp to feature; MODIFIER silent_mutation Average:72.477; most accessible tissue: Callus, score: 93.129 N N N N
vg0127041496 A -> G LOC_Os01g47310.1 downstream_gene_variant ; 2913.0bp to feature; MODIFIER silent_mutation Average:72.477; most accessible tissue: Callus, score: 93.129 N N N N
vg0127041496 A -> G LOC_Os01g47310-LOC_Os01g47330 intergenic_region ; MODIFIER silent_mutation Average:72.477; most accessible tissue: Callus, score: 93.129 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0127041496 NA 5.32E-07 mr1040 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
vg0127041496 NA 4.08E-06 mr1398 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
vg0127041496 NA 3.02E-08 mr1514 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
vg0127041496 NA 5.69E-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
vg0127041496 NA 1.58E-07 mr1850 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
vg0127041496 NA 1.16E-15 mr1040_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
vg0127041496 1.55E-06 4.48E-09 mr1398_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
vg0127041496 NA 9.35E-08 mr1422_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
vg0127041496 NA 1.32E-06 mr1583_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
vg0127041496 NA 1.13E-07 mr1696_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
vg0127041496 NA 1.05E-09 mr1916_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