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Detailed information for vg0503927501:

Variant ID: vg0503927501 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 3927501
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


GTTAAGTTCCAAATCTTGTCGGGATGAAAGTGCATCGCCATTGCTTCAATTTGATGGACCGATGAAGTTTTAGTCTTCAAAGTCAGGGCATCTGTAAATC[T/C]
GAGAAATGTTGGTTATTTTTCAAGGACAACAGTTCAAAGGTTCTCAGTCAGGCGAAAATAAGACTACCCACTGTAAGGGGGGGGTAGGTCTCTGAGATGA

Reverse complement sequence

TCATCTCAGAGACCTACCCCCCCCTTACAGTGGGTAGTCTTATTTTCGCCTGACTGAGAACCTTTGAACTGTTGTCCTTGAAAAATAACCAACATTTCTC[A/G]
GATTTACAGATGCCCTGACTTTGAAGACTAAAACTTCATCGGTCCATCAAATTGAAGCAATGGCGATGCACTTTCATCCCGACAAGATTTGGAACTTAAC

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 28.30% 8.70% 20.23% 42.74% NA
All Indica  2759 32.70% 1.20% 17.36% 48.79% NA
All Japonica  1512 23.00% 24.70% 15.21% 37.10% NA
Aus  269 17.10% 0.00% 52.04% 30.86% NA
Indica I  595 29.20% 0.20% 6.72% 63.87% NA
Indica II  465 32.30% 3.20% 18.92% 45.59% NA
Indica III  913 39.00% 0.30% 20.37% 40.31% NA
Indica Intermediate  786 28.10% 1.80% 20.99% 49.11% NA
Temperate Japonica  767 19.20% 41.70% 15.51% 23.60% NA
Tropical Japonica  504 22.80% 3.20% 14.88% 59.13% NA
Japonica Intermediate  241 35.70% 15.40% 14.94% 34.02% NA
VI/Aromatic  96 20.80% 0.00% 73.96% 5.21% NA
Intermediate  90 25.60% 6.70% 40.00% 27.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0503927501 T -> DEL N N silent_mutation Average:15.59; most accessible tissue: Minghui63 root, score: 19.68 N N N N
vg0503927501 T -> C LOC_Os05g07360-LOC_Os05g07380 intergenic_region ; MODIFIER silent_mutation Average:15.59; most accessible tissue: Minghui63 root, score: 19.68 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0503927501 7.71E-06 NA Grain_thickness 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
vg0503927501 7.13E-07 1.57E-21 Heading_date All YES 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
vg0503927501 NA 1.59E-17 Heading_date Jap_All YES 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
vg0503927501 NA 2.83E-17 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
vg0503927501 NA 6.33E-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
vg0503927501 NA 2.54E-07 mr1354 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
vg0503927501 NA 4.74E-10 mr1002_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
vg0503927501 NA 4.79E-06 mr1354_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
vg0503927501 NA 1.66E-06 mr1359_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
vg0503927501 NA 4.83E-06 mr1757_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
vg0503927501 NA 5.82E-06 mr1902_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