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Detailed information for vg0123406476:

Variant ID: vg0123406476 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23406476
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATCTTTGACACCTCCGAAGATCATCTCCCTATACAGAGTTTTGGTAGTAAATTCTCCTGTTTTTGTCAATTTCCATATCATTGTGTCTTTGTTAGAAGT[T/C]
AGCTGTATGTCTCTTAGTTTCTCATGCAAATCATTCCACTCCCCTACTTCTCTGTTTCCAATTGTTCTTCTTATACCAATCTCCCATTCCCCCCAGTGTT

Reverse complement sequence

AACACTGGGGGGAATGGGAGATTGGTATAAGAAGAACAATTGGAAACAGAGAAGTAGGGGAGTGGAATGATTTGCATGAGAAACTAAGAGACATACAGCT[A/G]
ACTTCTAACAAAGACACAATGATATGGAAATTGACAAAAACAGGAGAATTTACTACCAAAACTCTGTATAGGGAGATGATCTTCGGAGGTGTCAAAGATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.10% 24.90% 0.00% 0.00% NA
All Indica  2759 85.00% 15.00% 0.00% 0.00% NA
All Japonica  1512 52.40% 47.60% 0.00% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 91.80% 8.20% 0.00% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 71.90% 28.10% 0.00% 0.00% NA
Indica Intermediate  786 88.70% 11.30% 0.00% 0.00% NA
Temperate Japonica  767 37.20% 62.80% 0.00% 0.00% NA
Tropical Japonica  504 81.70% 18.30% 0.00% 0.00% NA
Japonica Intermediate  241 39.80% 60.20% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0123406476 T -> C LOC_Os01g41370.1 upstream_gene_variant ; 2147.0bp to feature; MODIFIER silent_mutation Average:41.817; most accessible tissue: Callus, score: 69.373 N N N N
vg0123406476 T -> C LOC_Os01g41360.1 downstream_gene_variant ; 2354.0bp to feature; MODIFIER silent_mutation Average:41.817; most accessible tissue: Callus, score: 69.373 N N N N
vg0123406476 T -> C LOC_Os01g41360-LOC_Os01g41370 intergenic_region ; MODIFIER silent_mutation Average:41.817; most accessible tissue: Callus, score: 69.373 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123406476 9.37E-07 NA mr1071 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
vg0123406476 NA 1.39E-06 mr1078 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
vg0123406476 4.35E-06 NA mr1140 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
vg0123406476 NA 7.26E-08 mr1193 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
vg0123406476 NA 9.13E-06 mr1202 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
vg0123406476 5.11E-06 NA mr1203 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
vg0123406476 NA 1.72E-06 mr1359 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
vg0123406476 NA 1.88E-06 mr1359 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
vg0123406476 NA 7.00E-06 mr1377 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
vg0123406476 NA 8.58E-06 mr1441 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
vg0123406476 1.00E-06 NA mr1467 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
vg0123406476 1.73E-06 NA mr1618 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
vg0123406476 NA 2.97E-06 mr1837 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