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Detailed information for vg0709322599:

Variant ID: vg0709322599 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 9322599
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTTCTATTTGGGTTCTCAAAAGAGGTTGAATATCCAGGGTGTTTATCTGCCCATGAGGTACTATATGTAGGTTCAGCTGGGCTATTTCCTCTTTAAGCT[C/A]
GGGAGCCATTCCTTCCATTCTCAGATGATTGCAATGGCTCTTACGACTCAAAGCGTCGGCCACAACGTTTGCTTTGCCGGGGTGGTAGTGAACCTCTAGA

Reverse complement sequence

TCTAGAGGTTCACTACCACCCCGGCAAAGCAAACGTTGTGGCCGACGCTTTGAGTCGTAAGAGCCATTGCAATCATCTGAGAATGGAAGGAATGGCTCCC[G/T]
AGCTTAAAGAGGAAATAGCCCAGCTGAACCTACATATAGTACCTCATGGGCAGATAAACACCCTGGATATTCAACCTCTTTTGAGAACCCAAATAGAAGA

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 84.20% 12.70% 3.03% 0.00% NA
All Indica  2759 74.70% 21.50% 3.77% 0.00% NA
All Japonica  1512 98.10% 0.10% 1.79% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 94.80% 2.50% 2.69% 0.00% NA
Indica II  465 67.10% 25.40% 7.53% 0.00% NA
Indica III  913 68.10% 31.00% 0.88% 0.00% NA
Indica Intermediate  786 71.80% 22.50% 5.73% 0.00% NA
Temperate Japonica  767 98.60% 0.10% 1.30% 0.00% NA
Tropical Japonica  504 96.80% 0.00% 3.17% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 78.90% 8.90% 12.22% 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
vg0709322599 C -> A LOC_Os07g16000.1 stop_gained ; p.Glu1185*; HIGH stop_gained Average:23.786; most accessible tissue: Minghui63 flag leaf, score: 31.47 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0709322599 NA 6.07E-07 mr1157 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
vg0709322599 NA 4.28E-08 mr1328 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
vg0709322599 NA 1.77E-06 mr1328 Ind_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
vg0709322599 NA 7.10E-09 mr1446 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
vg0709322599 NA 1.71E-06 mr1446 Ind_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
vg0709322599 NA 2.64E-06 mr1689 Ind_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
vg0709322599 3.71E-06 8.42E-12 mr1446_2 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
vg0709322599 5.29E-06 2.60E-09 mr1446_2 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
vg0709322599 NA 3.91E-06 mr1567_2 Ind_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