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Detailed information for vg0129349785:

Variant ID: vg0129349785 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 29349785
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 28. )

Flanking Sequence (100 bp) in Reference Genome:


ATTTGCACTTTGAACCACGCCATGCTATCAAGAGCCAGGCCCTCGCCGATTTTGTGGCAGAGTGGACCCCAGCTCCCGGGCCCGTCTCAGTCCCCGAGGC[T/C]
AGCTCGGGCCCCTCGCAGCTGCCTCACACGCCCACTGGGTGATGCAGTTCGACGGCTCCCTGTCTCTTCAGGGCGCCGGTGCGGGGGTCACGTTGACCTC

Reverse complement sequence

GAGGTCAACGTGACCCCCGCACCGGCGCCCTGAAGAGACAGGGAGCCGTCGAACTGCATCACCCAGTGGGCGTGTGAGGCAGCTGCGAGGGGCCCGAGCT[A/G]
GCCTCGGGGACTGAGACGGGCCCGGGAGCTGGGGTCCACTCTGCCACAAAATCGGCGAGGGCCTGGCTCTTGATAGCATGGCGTGGTTCAAAGTGCAAAT

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 41.10% 20.80% 26.30% 11.81% NA
All Indica  2759 57.50% 2.20% 36.97% 3.30% NA
All Japonica  1512 17.70% 58.80% 4.17% 19.31% NA
Aus  269 9.70% 3.70% 42.75% 43.87% NA
Indica I  595 34.50% 2.20% 58.99% 4.37% NA
Indica II  465 49.50% 1.70% 45.38% 3.44% NA
Indica III  913 79.40% 2.50% 15.88% 2.19% NA
Indica Intermediate  786 54.30% 2.20% 39.82% 3.69% NA
Temperate Japonica  767 2.30% 92.00% 0.13% 5.48% NA
Tropical Japonica  504 35.90% 14.70% 10.32% 39.09% NA
Japonica Intermediate  241 28.60% 45.20% 4.15% 21.99% NA
VI/Aromatic  96 35.40% 0.00% 18.75% 45.83% NA
Intermediate  90 28.90% 26.70% 30.00% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0129349785 T -> DEL N N silent_mutation Average:16.63; most accessible tissue: Callus, score: 29.634 N N N N
vg0129349785 T -> C LOC_Os01g51080.1 downstream_gene_variant ; 1561.0bp to feature; MODIFIER silent_mutation Average:16.63; most accessible tissue: Callus, score: 29.634 N N N N
vg0129349785 T -> C LOC_Os01g51100.1 downstream_gene_variant ; 2898.0bp to feature; MODIFIER silent_mutation Average:16.63; most accessible tissue: Callus, score: 29.634 N N N N
vg0129349785 T -> C LOC_Os01g51090.1 intron_variant ; MODIFIER silent_mutation Average:16.63; most accessible tissue: Callus, score: 29.634 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0129349785 NA 2.64E-06 mr1011 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
vg0129349785 NA 3.78E-13 mr1013 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
vg0129349785 NA 6.61E-15 mr1031 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
vg0129349785 NA 7.74E-06 mr1031 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
vg0129349785 NA 2.15E-12 mr1034 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
vg0129349785 NA 1.07E-15 mr1056 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
vg0129349785 NA 5.65E-06 mr1056 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
vg0129349785 NA 9.03E-06 mr1277 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
vg0129349785 NA 4.39E-07 mr1291 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
vg0129349785 NA 8.25E-10 mr1232_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
vg0129349785 NA 5.27E-26 mr1653_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
vg0129349785 NA 1.56E-07 mr1676_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
vg0129349785 NA 3.67E-08 mr1681_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
vg0129349785 NA 8.27E-22 mr1682_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
vg0129349785 NA 2.44E-07 mr1683_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