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Detailed information for vg0815303600:

Variant ID: vg0815303600 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 15303600
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: 363. )

Flanking Sequence (100 bp) in Reference Genome:


TGATGTGGCCAAGTGTGACAAAATCTTTGATTATCTTTTACAAGAAAAACAAATTATATTACCTAAAGGCCATGTCATACCATCTCAAGAAGAGTTGAAA[C/T]
GTCGAGCATATTGTAAATGGCATGATTCTCATTCTCATTCTACTAATGATTGCAATGTGTTTCGACGACAGGTTCAATCGGCCATAGATGAAGGACGATT

Reverse complement sequence

AATCGTCCTTCATCTATGGCCGATTGAACCTGTCGTCGAAACACATTGCAATCATTAGTAGAATGAGAATGAGAATCATGCCATTTACAATATGCTCGAC[G/A]
TTTCAACTCTTCTTGAGATGGTATGACATGGCCTTTAGGTAATATAATTTGTTTTTCTTGTAAAAGATAATCAAAGATTTTGTCACACTTGGCCACATCA

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 98.70% 1.30% 0.00% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 95.80% 4.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 92.20% 7.80% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0815303600 C -> T LOC_Os08g25180.1 downstream_gene_variant ; 4257.0bp to feature; MODIFIER silent_mutation Average:32.662; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N
vg0815303600 C -> T LOC_Os08g25190.1 intron_variant ; MODIFIER silent_mutation Average:32.662; most accessible tissue: Minghui63 panicle, score: 56.842 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0815303600 NA 4.72E-07 mr1028 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
vg0815303600 5.47E-06 5.46E-06 mr1373 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
vg0815303600 NA 9.42E-06 mr1453 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
vg0815303600 NA 1.04E-06 mr1648 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
vg0815303600 4.23E-08 6.33E-10 mr1697 Jap_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