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Detailed information for vg0506104260:

Variant ID: vg0506104260 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6104260
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: 123. )

Flanking Sequence (100 bp) in Reference Genome:


AAACTCTCCTATTTTTTTCAAAAGACGTTCAGTGGCTCGGGAAACGTGTGTGTGAAGATCGAGAAATCTTTCCTCTCTATTTTATTGTTTCAAACGCTGT[C/T]
ATTGGTTGGTCCCTAGTCAAATTTGCTTTGTACTAGTAATTAGAAGTCGGATTTCTATCTATTATTTAAAATATATTTGTTTGTAGTTATTTTCTTAAAG

Reverse complement sequence

CTTTAAGAAAATAACTACAAACAAATATATTTTAAATAATAGATAGAAATCCGACTTCTAATTACTAGTACAAAGCAAATTTGACTAGGGACCAACCAAT[G/A]
ACAGCGTTTGAAACAATAAAATAGAGAGGAAAGATTTCTCGATCTTCACACACACGTTTCCCGAGCCACTGAACGTCTTTTGAAAAAAATAGGAGAGTTT

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 95.90% 2.90% 1.18% 0.00% NA
All Indica  2759 93.20% 4.90% 1.96% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.00% 0.30% 3.70% 0.00% NA
Indica II  465 73.80% 22.60% 3.66% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 94.90% 3.30% 1.78% 0.00% NA
Temperate Japonica  767 99.70% 0.10% 0.13% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 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 97.80% 1.10% 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
vg0506104260 C -> T LOC_Os05g10940-LOC_Os05g10950 intergenic_region ; MODIFIER silent_mutation Average:40.264; most accessible tissue: Minghui63 panicle, score: 73.225 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506104260 NA 1.43E-12 mr1039 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
vg0506104260 NA 2.33E-07 mr1133 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
vg0506104260 NA 8.95E-06 mr1269 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
vg0506104260 NA 1.96E-07 mr1632 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
vg0506104260 NA 2.31E-06 mr1667 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
vg0506104260 NA 3.51E-14 mr1039_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
vg0506104260 NA 6.43E-06 mr1133_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
vg0506104260 2.11E-08 9.75E-16 mr1632_2 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