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Detailed information for vg0615688331:

Variant ID: vg0615688331 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 15688331
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:


ATCCTGATCCTAGGCGTCAGAGGGTGAACTATTTGAAGAATCTGCCCAAGTGTGGAAAGGATAGAATGATGAGTCCTGACACAATGCCTGCTGACTCTCA[G/A]
GATGACAGATTCAGGACCTTGGTACAGGTTGATTGGTATAATTCTGTGATCATGGGAAGATCTCATCCAGTGGTAGAGATGAAGTGGCTAGACTGGCAGT

Reverse complement sequence

ACTGCCAGTCTAGCCACTTCATCTCTACCACTGGATGAGATCTTCCCATGATCACAGAATTATACCAATCAACCTGTACCAAGGTCCTGAATCTGTCATC[C/T]
TGAGAGTCAGCAGGCATTGTGTCAGGACTCATCATTCTATCCTTTCCACACTTGGGCAGATTCTTCAAATAGTTCACCCTCTGACGCCTAGGATCAGGAT

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 96.90% 2.30% 0.83% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 90.40% 7.10% 2.51% 0.00% NA
Aus  269 100.00% 0.00% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.00% 0.13% 0.00% NA
Temperate Japonica  767 81.40% 14.00% 4.69% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.00% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0615688331 G -> A LOC_Os06g27710.1 synonymous_variant ; p.Gln6Gln; LOW synonymous_codon Average:59.933; most accessible tissue: Zhenshan97 flag leaf, score: 78.761 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0615688331 8.95E-06 8.95E-06 mr1038 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
vg0615688331 NA 1.69E-06 mr1045 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
vg0615688331 NA 2.59E-06 mr1358 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
vg0615688331 2.83E-07 2.83E-07 mr1389 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
vg0615688331 NA 7.61E-06 mr1305_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
vg0615688331 NA 2.14E-06 mr1585_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