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Detailed information for vg0627801195:

Variant ID: vg0627801195 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 27801195
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, A: 0.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


CAATCAACATCAGCTATGATATATATATCTCATCTCAAATGCTATTTTCCCTACATATATAGATTGATCCAACCACCTATGGTGACAGCAAAACCCACTT[C/A]
TTTGTATCTTGGACGGTATGTGTCCACTTATATTCATTGTTTGTGCACTTGAAATACATTGCTTAATTACCATGCATATGTCTTTAATTACAAGGTTTTG

Reverse complement sequence

CAAAACCTTGTAATTAAAGACATATGCATGGTAATTAAGCAATGTATTTCAAGTGCACAAACAATGAATATAAGTGGACACATACCGTCCAAGATACAAA[G/T]
AAGTGGGTTTTGCTGTCACCATAGGTGGTTGGATCAATCTATATATGTAGGGAAAATAGCATTTGAGATGAGATATATATATCATAGCTGATGTTGATTG

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 94.10% 5.90% 0.00% 0.00% NA
All Indica  2759 97.10% 2.90% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 29.40% 70.60% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.10% 1.90% 0.00% 0.00% NA
Indica III  913 95.70% 4.30% 0.00% 0.00% NA
Indica Intermediate  786 96.20% 3.80% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0627801195 C -> A LOC_Os06g45920.1 missense_variant ; p.Phe57Leu; MODERATE nonsynonymous_codon ; F57L Average:54.864; most accessible tissue: Callus, score: 84.596 unknown unknown TOLERATED 0.16

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0627801195 NA 7.56E-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
vg0627801195 NA 4.00E-09 mr1348 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