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Detailed information for vg0727624200:

Variant ID: vg0727624200 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 27624200
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TTTACCGGTCAATTCCTTCAATCTTGTCTTCAACCTCAGAGTAGAGCTCCCTGAGCTTTTCCAAGTTTTCCTCTGATGTTTCCCATTAGCCTCTACCACT[G/A]
GCTTCTAGGCAGGTCTGAACTAGCTTCCTGAATGAATTGGGGTTAGTGTCCATGAGCCTCTTCCTCATAGCCTCATCTTCAATAAATGTGGCATTTGCCT

Reverse complement sequence

AGGCAAATGCCACATTTATTGAAGATGAGGCTATGAGGAAGAGGCTCATGGACACTAACCCCAATTCATTCAGGAAGCTAGTTCAGACCTGCCTAGAAGC[C/T]
AGTGGTAGAGGCTAATGGGAAACATCAGAGGAAAACTTGGAAAAGCTCAGGGAGCTCTACTCTGAGGTTGAAGACAAGATTGAAGGAATTGACCGGTAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 3.20% 0.06% 0.00% NA
All Indica  2759 99.30% 0.70% 0.00% 0.00% NA
All Japonica  1512 96.50% 3.30% 0.20% 0.00% NA
Aus  269 70.30% 29.70% 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 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.80% 0.00% 0.00% NA
Temperate Japonica  767 93.70% 5.90% 0.39% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0727624200 G -> A LOC_Os07g46310.1 synonymous_variant ; p.Ala756Ala; LOW synonymous_codon Average:49.72; most accessible tissue: Minghui63 flower, score: 63.841 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0727624200 NA 7.43E-08 mr1126 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
vg0727624200 NA 4.81E-06 mr1286 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
vg0727624200 NA 7.82E-07 mr1321 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
vg0727624200 NA 1.01E-07 mr1665 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
vg0727624200 3.73E-06 3.73E-06 mr1815 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
vg0727624200 1.51E-06 1.51E-06 mr1981 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