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Detailed information for vg0901332646:

Variant ID: vg0901332646 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 1332646
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TAACTACTCCCTCCGTTCTAAAAAAAAAGTCAAACCCTAGGTTTCCGTGTCTAACTTTAACTGTCCGTCTTATATGAAATTTTTTTATAATTCGTATTTT[C/T]
ATTATTGTTAGATGATAAAACATGATTAATATTTTATGCATGACTTGTCTTTTTATTTTTTTTCATAATTTTTTCAAATAAGATGGATGATCAAACATTG

Reverse complement sequence

CAATGTTTGATCATCCATCTTATTTGAAAAAATTATGAAAAAAAATAAAAAGACAAGTCATGCATAAAATATTAATCATGTTTTATCATCTAACAATAAT[G/A]
AAAATACGAATTATAAAAAAATTTCATATAAGACGGACAGTTAAAGTTAGACACGGAAACCTAGGGTTTGACTTTTTTTTTAGAACGGAGGGAGTAGTTA

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 85.90% 14.10% 0.00% 0.00% NA
All Indica  2759 96.90% 3.10% 0.00% 0.00% NA
All Japonica  1512 65.80% 34.20% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 92.90% 7.10% 0.00% 0.00% NA
Indica III  913 98.50% 1.50% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.90% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 23.60% 76.40% 0.00% 0.00% NA
Japonica Intermediate  241 52.70% 47.30% 0.00% 0.00% NA
VI/Aromatic  96 54.20% 45.80% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0901332646 C -> T LOC_Os09g02850.1 upstream_gene_variant ; 4664.0bp to feature; MODIFIER silent_mutation Average:76.592; most accessible tissue: Zhenshan97 root, score: 86.79 N N N N
vg0901332646 C -> T LOC_Os09g02840.1 intron_variant ; MODIFIER silent_mutation Average:76.592; most accessible tissue: Zhenshan97 root, score: 86.79 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0901332646 2.15E-07 NA Grain_width All YES 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
vg0901332646 NA 2.00E-13 Grain_width 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
vg0901332646 NA 9.45E-07 mr1229 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
vg0901332646 NA 2.43E-06 mr1295 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
vg0901332646 NA 5.28E-06 mr1596 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
vg0901332646 NA 4.80E-08 mr1993 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