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Detailed information for vg0631155509:

Variant ID: vg0631155509 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 31155509
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 340. )

Flanking Sequence (100 bp) in Reference Genome:


TCAGTTCTCCTCAGCTGTGCCTTCTTTTATGACATCTTCTGGGTGTTTGTCTCCAAGAGATGGTTTCATGAGAGCGTGATGATCGTGGTAAGTTTTGTGG[A/G]
AATTTATTCTAGACTTCTGGTAATTGGTGATCTCATTGTTTAAGCTAAGTTGGTTATGCTGGTGTGCTTCTCAAAGGTAGCTCGTGGTGACAAGACTGAT

Reverse complement sequence

ATCAGTCTTGTCACCACGAGCTACCTTTGAGAAGCACACCAGCATAACCAACTTAGCTTAAACAATGAGATCACCAATTACCAGAAGTCTAGAATAAATT[T/C]
CCACAAAACTTACCACGATCATCACGCTCTCATGAAACCATCTCTTGGAGACAAACACCCAGAAGATGTCATAAAAGAAGGCACAGCTGAGGAGAACTGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.00% 2.90% 2.14% 0.00% NA
All Indica  2759 91.40% 5.00% 3.59% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 74.10% 15.30% 10.59% 0.00% NA
Indica II  465 94.00% 3.20% 2.80% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 93.40% 3.90% 2.67% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0631155509 A -> G LOC_Os06g51440.1 upstream_gene_variant ; 1820.0bp to feature; MODIFIER silent_mutation Average:69.746; most accessible tissue: Callus, score: 85.647 N N N N
vg0631155509 A -> G LOC_Os06g51420.1 downstream_gene_variant ; 4964.0bp to feature; MODIFIER silent_mutation Average:69.746; most accessible tissue: Callus, score: 85.647 N N N N
vg0631155509 A -> G LOC_Os06g51430.1 intron_variant ; MODIFIER silent_mutation Average:69.746; most accessible tissue: Callus, score: 85.647 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0631155509 NA 8.18E-11 Heading_date Ind_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
vg0631155509 4.83E-08 3.30E-17 mr1038 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
vg0631155509 4.92E-07 3.70E-16 mr1038 Ind_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
vg0631155509 NA 1.11E-06 mr1125 Ind_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
vg0631155509 1.60E-10 1.13E-22 mr1389 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
vg0631155509 1.26E-08 4.49E-19 mr1389 Ind_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
vg0631155509 NA 1.85E-06 mr1627 Ind_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
vg0631155509 NA 2.99E-06 mr1002_2 Ind_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
vg0631155509 4.57E-11 2.38E-25 mr1038_2 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
vg0631155509 8.30E-10 1.98E-22 mr1038_2 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
vg0631155509 NA 3.29E-07 mr1125_2 Ind_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
vg0631155509 1.12E-06 NA mr1141_2 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
vg0631155509 6.62E-06 3.67E-09 mr1141_2 Ind_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
vg0631155509 NA 2.48E-06 mr1152_2 Ind_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
vg0631155509 4.63E-09 1.31E-21 mr1389_2 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
vg0631155509 1.65E-07 1.18E-19 mr1389_2 Ind_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
vg0631155509 NA 7.50E-07 mr1653_2 Ind_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
vg0631155509 NA 2.56E-06 mr1864_2 Ind_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