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Detailed information for vg0330452376:

Variant ID: vg0330452376 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 30452376
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTGCATATTTGTGATTAGGGGTTCTATAACTGTCCGTCTGCGAAGATCCATTATGACAGTCGGCTCACTTAAAGAGGCTGTCTATGAAACATAATCTT[C/T]
ATAGGCGGCCCACTACCCGTAGACCCACATAATCCATTTTAGCCTTCTATAAAAATTGTTTTCATAGTAGTTACATTTTCCTAACAATCTTCCATGCAGG

Reverse complement sequence

CCTGCATGGAAGATTGTTAGGAAAATGTAACTACTATGAAAACAATTTTTATAGAAGGCTAAAATGGATTATGTGGGTCTACGGGTAGTGGGCCGCCTAT[G/A]
AAGATTATGTTTCATAGACAGCCTCTTTAAGTGAGCCGACTGTCATAATGGATCTTCGCAGACGGACAGTTATAGAACCCCTAATCACAAATATGCAGGC

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 94.10% 4.50% 1.38% 0.00% NA
All Indica  2759 90.00% 7.70% 2.28% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 65.20% 27.40% 7.39% 0.00% NA
Indica II  465 97.40% 1.70% 0.86% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 92.90% 5.30% 1.78% 0.00% NA
Temperate Japonica  767 99.90% 0.00% 0.13% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 2.20% 1.11% 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
vg0330452376 C -> T LOC_Os03g53090.1 downstream_gene_variant ; 2195.0bp to feature; MODIFIER silent_mutation Average:66.131; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0330452376 C -> T LOC_Os03g53110.1 downstream_gene_variant ; 1383.0bp to feature; MODIFIER silent_mutation Average:66.131; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0330452376 C -> T LOC_Os03g53100.1 intron_variant ; MODIFIER silent_mutation Average:66.131; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0330452376 1.45E-09 3.45E-16 mr1038 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
vg0330452376 1.34E-08 1.67E-15 mr1038 Ind_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
vg0330452376 4.05E-11 3.15E-19 mr1389 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
vg0330452376 3.46E-10 8.44E-18 mr1389 Ind_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
vg0330452376 9.69E-07 1.38E-17 mr1038_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
vg0330452376 9.12E-07 8.53E-17 mr1038_2 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
vg0330452376 4.08E-07 2.84E-16 mr1389_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
vg0330452376 4.34E-07 1.28E-16 mr1389_2 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