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Detailed information for vg0623156624:

Variant ID: vg0623156624 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 23156624
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.65, G: 0.34, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:


TGGAAGCGACAGATTTGCGGTGGCGACGACGACGATGATGGTGGCGATGGCCATTGCGAGGATGACGACTGTAGTGATGGCTGCGACGACGATGGCTTCG[G/A]
GAGCTAGGTTTTAGGGATGAATTGAGGGCTAGAGCTTTGATTTTCGGAATTTTTATATTTTTTTGGCGATTTTTCATTTTTGCATGCGGGCAGCTTAAGC

Reverse complement sequence

GCTTAAGCTGCCCGCATGCAAAAATGAAAAATCGCCAAAAAAATATAAAAATTCCGAAAATCAAAGCTCTAGCCCTCAATTCATCCCTAAAACCTAGCTC[C/T]
CGAAGCCATCGTCGTCGCAGCCATCACTACAGTCGTCATCCTCGCAATGGCCATCGCCACCATCATCGTCGTCGTCGCCACCGCAAATCTGTCGCTTCCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.90% 36.10% 0.02% 0.00% NA
All Indica  2759 95.90% 4.10% 0.00% 0.00% NA
All Japonica  1512 3.90% 96.10% 0.00% 0.00% NA
Aus  269 95.90% 4.10% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 92.90% 7.10% 0.00% 0.00% NA
Indica III  913 96.50% 3.50% 0.00% 0.00% NA
Indica Intermediate  786 94.40% 5.60% 0.00% 0.00% NA
Temperate Japonica  767 2.00% 98.00% 0.00% 0.00% NA
Tropical Japonica  504 7.30% 92.70% 0.00% 0.00% NA
Japonica Intermediate  241 2.90% 97.10% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 50.00% 48.90% 1.11% 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
vg0623156624 G -> A LOC_Os06g39000.1 missense_variant ; p.Gly139Glu; MODERATE nonsynonymous_codon ; G139E Average:62.228; most accessible tissue: Zhenshan97 panicle, score: 71.253 unknown unknown DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0623156624 NA 2.37E-10 mr1070 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
vg0623156624 NA 2.30E-27 mr1072 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
vg0623156624 NA 2.90E-28 mr1075 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
vg0623156624 NA 1.26E-28 mr1202 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
vg0623156624 NA 2.86E-22 mr1254 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
vg0623156624 NA 3.23E-29 mr1256 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
vg0623156624 NA 1.16E-07 mr1805 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
vg0623156624 NA 3.28E-53 mr1861 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
vg0623156624 NA 1.31E-15 mr1933 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
vg0623156624 9.64E-07 3.57E-06 mr1973 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
vg0623156624 NA 3.00E-56 mr1124_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