\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0504314615:

Variant ID: vg0504314615 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 4314615
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GCACTCCCTCCTCATTTCTCCTCATCTCGACTCTGATTAAAAAAACAGACAGAGGGGGAGGAGAAGAGAAGAAGAGGCGAAGCCCTGCCGATTTGAGATC[C/T]
GATTTCAGGTAATATTTATAGATCCTATATGTGACTATTTAGTTAACTAGTGTGTATTTTTTAAAACTTTGTTTGAATAAATGCATTATACTCCCTCCAT

Reverse complement sequence

ATGGAGGGAGTATAATGCATTTATTCAAACAAAGTTTTAAAAAATACACACTAGTTAACTAAATAGTCACATATAGGATCTATAAATATTACCTGAAATC[G/A]
GATCTCAAATCGGCAGGGCTTCGCCTCTTCTTCTCTTCTCCTCCCCCTCTGTCTGTTTTTTTAATCAGAGTCGAGATGAGGAGAAATGAGGAGGGAGTGC

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 62.50% 37.30% 0.28% 0.00% NA
All Indica  2759 39.30% 60.30% 0.47% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 78.10% 21.90% 0.00% 0.00% NA
Indica I  595 16.10% 83.70% 0.17% 0.00% NA
Indica II  465 56.30% 43.00% 0.65% 0.00% NA
Indica III  913 40.50% 59.00% 0.44% 0.00% NA
Indica Intermediate  786 45.20% 54.20% 0.64% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0504314615 C -> T LOC_Os05g07950.1 upstream_gene_variant ; 4193.0bp to feature; MODIFIER silent_mutation Average:73.701; most accessible tissue: Minghui63 root, score: 90.94 N N N N
vg0504314615 C -> T LOC_Os05g07960.1 upstream_gene_variant ; 257.0bp to feature; MODIFIER silent_mutation Average:73.701; most accessible tissue: Minghui63 root, score: 90.94 N N N N
vg0504314615 C -> T LOC_Os05g07970.1 upstream_gene_variant ; 662.0bp to feature; MODIFIER silent_mutation Average:73.701; most accessible tissue: Minghui63 root, score: 90.94 N N N N
vg0504314615 C -> T LOC_Os05g07980.1 downstream_gene_variant ; 2882.0bp to feature; MODIFIER silent_mutation Average:73.701; most accessible tissue: Minghui63 root, score: 90.94 N N N N
vg0504314615 C -> T LOC_Os05g07960-LOC_Os05g07970 intergenic_region ; MODIFIER silent_mutation Average:73.701; most accessible tissue: Minghui63 root, score: 90.94 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0504314615 2.20E-06 NA mr1117 Ind_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