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Detailed information for vg0100503766:

Variant ID: vg0100503766 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 503766
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, C: 0.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


GAGAGTAGGAATACAAGAATTAACCAAGTGTTTTACATCATATTATAGGAAAATAAGACATGACTGAGGAAATAATAAATCAGACAAACTGTCTGTAAAG[T/C]
TTTATTTACAATAAATGCTAATGTGATAGTCGTCAATTCAACGGTACTTGCCAATTGGCGCACCTTGGCCGATATTAAACTCTAGTGAGATCAACCCTGC

Reverse complement sequence

GCAGGGTTGATCTCACTAGAGTTTAATATCGGCCAAGGTGCGCCAATTGGCAAGTACCGTTGAATTGACGACTATCACATTAGCATTTATTGTAAATAAA[A/G]
CTTTACAGACAGTTTGTCTGATTTATTATTTCCTCAGTCATGTCTTATTTTCCTATAATATGATGTAAAACACTTGGTTAATTCTTGTATTCCTACTCTC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 5.40% 0.00% 0.00% NA
All Indica  2759 98.50% 1.50% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 29.40% 70.60% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 96.20% 3.80% 0.00% 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 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0100503766 T -> C LOC_Os01g01925.1 upstream_gene_variant ; 3504.0bp to feature; MODIFIER silent_mutation Average:41.734; most accessible tissue: Callus, score: 82.449 N N N N
vg0100503766 T -> C LOC_Os01g01920.1 intron_variant ; MODIFIER silent_mutation Average:41.734; most accessible tissue: Callus, score: 82.449 N N N N
vg0100503766 T -> C LOC_Os01g01920.2 intron_variant ; MODIFIER silent_mutation Average:41.734; most accessible tissue: Callus, score: 82.449 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0100503766 NA 3.87E-10 mr1415 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
vg0100503766 NA 4.03E-43 mr1549 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
vg0100503766 NA 1.65E-47 mr1550 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
vg0100503766 NA 3.87E-10 mr1567 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
vg0100503766 NA 1.55E-41 mr1757 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
vg0100503766 NA 1.62E-09 mr1166_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
vg0100503766 NA 8.42E-32 mr1549_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
vg0100503766 6.71E-06 5.88E-52 mr1550_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
vg0100503766 NA 3.88E-10 mr1567_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
vg0100503766 NA 7.46E-33 mr1757_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
vg0100503766 NA 1.99E-07 mr1762_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
vg0100503766 NA 1.73E-17 mr1961_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