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Detailed information for vg0128797626:

Variant ID: vg0128797626 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 28797626
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAACATGTAAGAACAGCTTGTCTGCTGAGTCATGACCGGTGATGTGTATGTGATGGAAGAAAACGTATGTACGACTTAATGCTTGCACCTATACTACT[G/C]
CTGTGTGCATTATTCGAGTGATCAATTTGAGCATTTGCAGCTCACAACCCTGCAGGTTTGTCTGTCTATATATGCACGTATGCGCAGCTCATTAGTGTTA

Reverse complement sequence

TAACACTAATGAGCTGCGCATACGTGCATATATAGACAGACAAACCTGCAGGGTTGTGAGCTGCAAATGCTCAAATTGATCACTCGAATAATGCACACAG[C/G]
AGTAGTATAGGTGCAAGCATTAAGTCGTACATACGTTTTCTTCCATCACATACACATCACCGGTCATGACTCAGCAGACAAGCTGTTCTTACATGTTTTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.80% 29.20% 0.00% 0.00% NA
All Indica  2759 98.90% 1.10% 0.00% 0.00% NA
All Japonica  1512 15.40% 84.60% 0.00% 0.00% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 0.00% 0.00% NA
Temperate Japonica  767 0.80% 99.20% 0.00% 0.00% NA
Tropical Japonica  504 41.50% 58.50% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.50% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 58.90% 41.10% 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
vg0128797626 G -> C LOC_Os01g50110.1 3_prime_UTR_variant ; 139.0bp to feature; MODIFIER silent_mutation Average:70.045; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N
vg0128797626 G -> C LOC_Os01g50100.1 upstream_gene_variant ; 4326.0bp to feature; MODIFIER silent_mutation Average:70.045; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N
vg0128797626 G -> C LOC_Os01g50120.1 upstream_gene_variant ; 1248.0bp to feature; MODIFIER silent_mutation Average:70.045; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N
vg0128797626 G -> C LOC_Os01g50120.2 upstream_gene_variant ; 1248.0bp to feature; MODIFIER silent_mutation Average:70.045; most accessible tissue: Zhenshan97 young leaf, score: 81.6 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0128797626 NA 7.54E-52 mr1241 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
vg0128797626 NA 3.15E-87 mr1334 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
vg0128797626 NA 7.65E-37 mr1486 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
vg0128797626 NA 9.29E-23 mr1548 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
vg0128797626 NA 8.69E-26 mr1805 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
vg0128797626 NA 1.92E-14 mr1277_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
vg0128797626 NA 8.79E-99 mr1334_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
vg0128797626 NA 4.52E-44 mr1486_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
vg0128797626 NA 7.91E-18 mr1682_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
vg0128797626 NA 4.24E-21 mr1698_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
vg0128797626 NA 9.50E-17 mr1730_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
vg0128797626 NA 5.40E-44 mr1805_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
vg0128797626 NA 4.54E-15 mr1866_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
vg0128797626 NA 3.31E-55 mr1991_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