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Detailed information for vg0705048171:

Variant ID: vg0705048171 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 5048171
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


GACAACAGGGTAGCCTTCCTCCTCAAGCTCGCGCCCGACGGAATCAGAGATAGTGCTAGATCCCTACGGCCGGCCTCTGAAGGTACCGGATAGGGTCGAT[C/T]
TAGGCGTATCTCTGATGTCGATATCCGGCGGCTTGTCTTGGCGTATGTAGGCTTCTATGTTGATTGTGTTGGGAGTTGATTGTCTCGTGGTGGGTCTCGA

Reverse complement sequence

TCGAGACCCACCACGAGACAATCAACTCCCAACACAATCAACATAGAAGCCTACATACGCCAAGACAAGCCGCCGGATATCGACATCAGAGATACGCCTA[G/A]
ATCGACCCTATCCGGTACCTTCAGAGGCCGGCCGTAGGGATCTAGCACTATCTCTGATTCCGTCGGGCGCGAGCTTGAGGAGGAAGGCTACCCTGTTGTC

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 95.10% 4.80% 0.13% 0.00% NA
All Indica  2759 93.10% 6.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 85.90% 11.90% 2.23% 0.00% NA
Indica I  595 89.10% 10.90% 0.00% 0.00% NA
Indica II  465 98.30% 1.70% 0.00% 0.00% NA
Indica III  913 92.00% 8.00% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.60% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 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% 3.30% 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
vg0705048171 C -> T LOC_Os07g09540.1 downstream_gene_variant ; 4059.0bp to feature; MODIFIER silent_mutation Average:39.115; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N
vg0705048171 C -> T LOC_Os07g09540-LOC_Os07g09560 intergenic_region ; MODIFIER silent_mutation Average:39.115; most accessible tissue: Zhenshan97 panicle, score: 59.59 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0705048171 3.04E-06 3.04E-06 mr1602 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