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Detailed information for vg0403256148:

Variant ID: vg0403256148 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 3256148
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.24, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:


AATATTTGCTTCATCCTTAAAACCACAATGGTAGTTTAAATTTGGGATGATGGGAGTATAGAAGATAGAGCACGCCGAGCGAGCCGGCGTTACTTTTAGC[T/C]
GATCGACTTTTATTATTTTCTTCCTTTTAGATTAGTTTTATCCGATAATGCTATTATTAGTAGCCTGAATCTATCAAAACATGGCAGCAATGATTGCTCA

Reverse complement sequence

TGAGCAATCATTGCTGCCATGTTTTGATAGATTCAGGCTACTAATAATAGCATTATCGGATAAAACTAATCTAAAAGGAAGAAAATAATAAAAGTCGATC[A/G]
GCTAAAAGTAACGCCGGCTCGCTCGGCGTGCTCTATCTTCTATACTCCCATCATCCCAAATTTAAACTACCATTGTGGTTTTAAGGATGAAGCAAATATT

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 70.50% 23.50% 3.41% 2.56% NA
All Indica  2759 81.80% 13.30% 2.50% 2.36% NA
All Japonica  1512 45.90% 46.20% 5.42% 2.51% NA
Aus  269 84.00% 8.60% 1.86% 5.58% NA
Indica I  595 64.70% 28.90% 6.05% 0.34% NA
Indica II  465 81.50% 12.90% 1.29% 4.30% NA
Indica III  913 94.90% 2.00% 0.55% 2.63% NA
Indica Intermediate  786 79.80% 15.00% 2.80% 2.42% NA
Temperate Japonica  767 16.70% 75.70% 5.35% 2.22% NA
Tropical Japonica  504 82.30% 10.90% 4.17% 2.58% NA
Japonica Intermediate  241 62.70% 25.70% 8.30% 3.32% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 72.20% 18.90% 5.56% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0403256148 T -> C LOC_Os04g06260.1 upstream_gene_variant ; 1653.0bp to feature; MODIFIER silent_mutation Average:14.55; most accessible tissue: Callus, score: 43.464 N N N N
vg0403256148 T -> C LOC_Os04g06244-LOC_Os04g06260 intergenic_region ; MODIFIER silent_mutation Average:14.55; most accessible tissue: Callus, score: 43.464 N N N N
vg0403256148 T -> DEL N N silent_mutation Average:14.55; most accessible tissue: Callus, score: 43.464 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0403256148 NA 7.20E-10 Heading_date Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0403256148 NA 3.70E-13 Plant_height Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0403256148 NA 1.66E-13 Spikelet_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0403256148 NA 1.27E-12 Spikelet_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0403256148 NA 7.44E-08 mr1252 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
vg0403256148 NA 6.66E-06 mr1521 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
vg0403256148 NA 4.25E-06 mr1576 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
vg0403256148 NA 5.81E-07 mr1729 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
vg0403256148 NA 4.52E-06 mr1851 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
vg0403256148 6.33E-06 NA mr1864 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
vg0403256148 NA 1.73E-12 mr1864 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
vg0403256148 NA 4.96E-20 mr1010_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
vg0403256148 NA 1.97E-08 mr1521_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
vg0403256148 NA 6.06E-09 mr1576_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