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Detailed information for vg0627801768:

Variant ID: vg0627801768 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27801768
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, C: 0.10, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AAAATGTACCTTGTATTTATAGTAGGAAAATATCTAAGTGTACAGCCTTTACTTTCTCGAATAGTAACTCTTCCGAATATTCTTGCGCGATGATATTTTT[C/A]
CATATATGTACACAGGACAAAAATGATGGAGATTGGTGGCTTTACTTTGGATATGACATCAACAATCTCAATCGAGTTGGATTTTGGCCAAAGAATATTT

Reverse complement sequence

AAATATTCTTTGGCCAAAATCCAACTCGATTGAGATTGTTGATGTCATATCCAAAGTAAAGCCACCAATCTCCATCATTTTTGTCCTGTGTACATATATG[G/T]
AAAAATATCATCGCGCAAGAATATTCGGAAGAGTTACTATTCGAGAAAGTAAAGGCTGTACACTTAGATATTTTCCTACTATAAATACAAGGTACATTTT

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 87.00% 13.00% 0.00% 0.00% NA
All Indica  2759 85.60% 14.40% 0.00% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 26.80% 73.20% 0.00% 0.00% NA
Indica I  595 95.00% 5.00% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 78.40% 21.60% 0.00% 0.00% NA
Indica Intermediate  786 79.80% 20.20% 0.00% 0.00% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0627801768 C -> A LOC_Os06g45910.1 downstream_gene_variant ; 3188.0bp to feature; MODIFIER silent_mutation Average:57.235; most accessible tissue: Callus, score: 80.193 N N N N
vg0627801768 C -> A LOC_Os06g45920.1 intron_variant ; MODIFIER silent_mutation Average:57.235; most accessible tissue: Callus, score: 80.193 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627801768 NA 3.96E-06 mr1184 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
vg0627801768 NA 6.53E-10 mr1388_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
vg0627801768 NA 6.31E-06 mr1511_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
vg0627801768 NA 6.47E-16 mr1587_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