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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1210393974:

Variant ID: vg1210393974 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 10393974
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 177. )

Flanking Sequence (100 bp) in Reference Genome:


TGTAATGGTGTCCTTCGCTTTAAAGGCAGAGTCTGGATAGATAACAATCCATCTGTGCAGGATAAGATTATCTCTGCGTTGCACAGTAGTCCTTTGGGGG[G/A]
GCACTCTGGTTTTCCTGTTACTTATAGTAAAATCAAGTCTCTTTTTGCTTGGCCCAAGATGAAGAAACAGATTCATACTGCTGTCAAAACATGTGGTATT

Reverse complement sequence

AATACCACATGTTTTGACAGCAGTATGAATCTGTTTCTTCATCTTGGGCCAAGCAAAAAGAGACTTGATTTTACTATAAGTAACAGGAAAACCAGAGTGC[C/T]
CCCCCAAAGGACTACTGTGCAACGCAGAGATAATCTTATCCTGCACAGATGGATTGTTATCTATCCAGACTCTGCCTTTAAAGCGAAGGACACCATTACA

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 74.40% 25.60% 0.04% 0.00% NA
All Indica  2759 72.50% 27.50% 0.07% 0.00% NA
All Japonica  1512 80.60% 19.40% 0.00% 0.00% NA
Aus  269 57.60% 42.40% 0.00% 0.00% NA
Indica I  595 88.90% 11.10% 0.00% 0.00% NA
Indica II  465 66.20% 33.80% 0.00% 0.00% NA
Indica III  913 67.70% 32.10% 0.22% 0.00% NA
Indica Intermediate  786 69.20% 30.80% 0.00% 0.00% NA
Temperate Japonica  767 95.30% 4.70% 0.00% 0.00% NA
Tropical Japonica  504 65.10% 34.90% 0.00% 0.00% NA
Japonica Intermediate  241 66.00% 34.00% 0.00% 0.00% NA
VI/Aromatic  96 81.20% 18.80% 0.00% 0.00% NA
Intermediate  90 73.30% 26.70% 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
vg1210393974 G -> A LOC_Os12g18080.1 missense_variant ; p.Gly1027Glu; MODERATE nonsynonymous_codon ; G1027E Average:39.878; most accessible tissue: Minghui63 flag leaf, score: 57.188 probably damaging 2.673 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1210393974 NA 2.55E-07 mr1179 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
vg1210393974 NA 2.13E-08 mr1229 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
vg1210393974 NA 2.79E-06 mr1328 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
vg1210393974 NA 2.05E-06 mr1338 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
vg1210393974 1.44E-07 1.44E-07 mr1663 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
vg1210393974 NA 1.67E-06 mr1668 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
vg1210393974 NA 1.53E-06 mr1671 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
vg1210393974 NA 8.11E-06 mr1268_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
vg1210393974 9.72E-06 1.13E-08 mr1425_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
vg1210393974 NA 5.56E-07 mr1425_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
vg1210393974 NA 2.62E-06 mr1425_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