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Detailed information for vg0105586222:

Variant ID: vg0105586222 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5586222
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 327. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTGGCACATGTTTTAACAAGAAGAAGAATGCAAAATTCCATGTAAATTGGTAGCATCGACTTGGATATCGATTGGTTCACCTGATCTAGAGTAATGGA[G/T]
TACATTTATGACTCCGCGTCGTAGATATATTTTTTCAGTAATTTTCTAATAATAGTTAGCGCTATTTCTTTGGTTAAAATTAGGTAACTTGTGTGATAAA

Reverse complement sequence

TTTATCACACAAGTTACCTAATTTTAACCAAAGAAATAGCGCTAACTATTATTAGAAAATTACTGAAAAAATATATCTACGACGCGGAGTCATAAATGTA[C/A]
TCCATTACTCTAGATCAGGTGAACCAATCGATATCCAAGTCGATGCTACCAATTTACATGGAATTTTGCATTCTTCTTCTTGTTAAAACATGTGCCAAAT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.60% 1.10% 0.30% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.80% 3.30% 0.93% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 93.40% 5.10% 1.56% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 3.30% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0105586222 G -> T LOC_Os01g10520.1 upstream_gene_variant ; 955.0bp to feature; MODIFIER silent_mutation Average:54.613; most accessible tissue: Minghui63 flower, score: 74.23 N N N N
vg0105586222 G -> T LOC_Os01g10520-LOC_Os01g10530 intergenic_region ; MODIFIER silent_mutation Average:54.613; most accessible tissue: Minghui63 flower, score: 74.23 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105586222 NA 1.08E-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
vg0105586222 NA 2.40E-06 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
vg0105586222 NA 3.21E-09 mr1757 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
vg0105586222 NA 1.53E-07 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
vg0105586222 4.19E-07 9.62E-12 mr1549_2 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
vg0105586222 NA 7.83E-06 mr1723_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
vg0105586222 NA 4.13E-10 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