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Detailed information for vg0110367769:

Variant ID: vg0110367769 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 10367769
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTGATGAATGAAATTGTTGGTTTATAATTTATACTCCCTCCGTTTCGAAATATTTGACGTCATTGACTTTTTTAAACATGTTTGACCGTTTGTCTTATT[C/T]
AAAAAATTTAAGTAATTATTAATTCTTTTCCTATCATTTGATTCATTGTTAAATATATTTTTATGTAGGCATATAATTTTACATATTTCACAAAATTTTT

Reverse complement sequence

AAAAATTTTGTGAAATATGTAAAATTATATGCCTACATAAAAATATATTTAACAATGAATCAAATGATAGGAAAAGAATTAATAATTACTTAAATTTTTT[G/A]
AATAAGACAAACGGTCAAACATGTTTAAAAAAGTCAATGACGTCAAATATTTCGAAACGGAGGGAGTATAAATTATAAACCAACAATTTCATTCATCAAA

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 60.90% 39.10% 0.02% 0.00% NA
All Indica  2759 93.60% 6.30% 0.04% 0.00% NA
All Japonica  1512 3.30% 96.70% 0.00% 0.00% NA
Aus  269 43.10% 56.90% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 90.30% 9.70% 0.00% 0.00% NA
Indica Intermediate  786 90.80% 9.00% 0.13% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 5.40% 94.60% 0.00% 0.00% NA
Japonica Intermediate  241 4.10% 95.90% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 15.60% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 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
vg0110367769 C -> T LOC_Os01g18440.1 downstream_gene_variant ; 438.0bp to feature; MODIFIER silent_mutation Average:39.559; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0110367769 C -> T LOC_Os01g18450.1 downstream_gene_variant ; 2293.0bp to feature; MODIFIER silent_mutation Average:39.559; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg0110367769 C -> T LOC_Os01g18440-LOC_Os01g18450 intergenic_region ; MODIFIER silent_mutation Average:39.559; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0110367769 NA 9.34E-49 mr1125 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
vg0110367769 NA 1.17E-25 mr1551 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
vg0110367769 NA 1.81E-28 mr1638 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
vg0110367769 NA 6.50E-62 mr1125_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
vg0110367769 NA 1.70E-37 mr1223_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
vg0110367769 NA 1.09E-06 mr1275_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
vg0110367769 NA 2.97E-24 mr1350_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
vg0110367769 NA 2.88E-09 mr1506_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
vg0110367769 NA 1.30E-07 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
vg0110367769 NA 1.41E-08 mr1751_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
vg0110367769 NA 6.10E-12 mr1781_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
vg0110367769 8.72E-07 NA mr1987_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