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Detailed information for vg0724166441:

Variant ID: vg0724166441 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 24166441
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, A: 0.02, T: 0.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


CCCTTTGTGAGTTCGGCCGGAGGCAGCGGGTGAGATTCGAGGGCTTGGTGAGCGGAGCTGTGTGATCTTGAGGGGGGTTAGCCCCCCCAAGACGATGAGA[A/C]
AAAAGAGGTTTATACAGATTCGGGCCGCTAAGAAGCGTAATACCCTACTCCTGTGCATGATTGATTGAATGTAGAACACAAGTGTTTGGGGTTGCGAGAC

Reverse complement sequence

GTCTCGCAACCCCAAACACTTGTGTTCTACATTCAATCAATCATGCACAGGAGTAGGGTATTACGCTTCTTAGCGGCCCGAATCTGTATAAACCTCTTTT[T/G]
TCTCATCGTCTTGGGGGGGCTAACCCCCCTCAAGATCACACAGCTCCGCTCACCAAGCCCTCGAATCTCACCCGCTGCCTCCGGCCGAACTCACAAAGGG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.00% 18.00% 0.00% 0.00% NA
All Indica  2759 98.60% 1.40% 0.00% 0.00% NA
All Japonica  1512 54.80% 45.20% 0.00% 0.00% NA
Aus  269 58.00% 42.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 97.20% 2.80% 0.00% 0.00% NA
Indica III  913 99.30% 0.70% 0.00% 0.00% NA
Indica Intermediate  786 98.10% 1.90% 0.00% 0.00% NA
Temperate Japonica  767 18.30% 81.70% 0.00% 0.00% NA
Tropical Japonica  504 95.60% 4.40% 0.00% 0.00% NA
Japonica Intermediate  241 85.90% 14.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0724166441 A -> C LOC_Os07g40300.1 downstream_gene_variant ; 1400.0bp to feature; MODIFIER silent_mutation Average:48.563; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N
vg0724166441 A -> C LOC_Os07g40300-LOC_Os07g40310 intergenic_region ; MODIFIER silent_mutation Average:48.563; most accessible tissue: Minghui63 panicle, score: 68.46 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0724166441 NA 1.11E-06 mr1182 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
vg0724166441 NA 8.16E-06 mr1639 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
vg0724166441 NA 3.08E-07 mr1763 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
vg0724166441 NA 1.41E-06 mr1182_2 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
vg0724166441 8.51E-06 NA mr1549_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
vg0724166441 2.22E-07 NA mr1691_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
vg0724166441 NA 8.58E-06 mr1959_2 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