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Detailed information for vg1223507277:

Variant ID: vg1223507277 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 23507277
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: 130. )

Flanking Sequence (100 bp) in Reference Genome:


CGACCTTGCTTTTATCTTGGGAGAGGTGGACTGGGTGTTGACTACCCCATGTCCTATAGAACCTGCTGAACTTATCAGAGGTGAAAATGAGTCAGATGCT[G/A]
ACTGGCAAAAGAGACAGAGGGACAATGCTCCTCTCGTCATGTCGTATGACATTGAACAAAAGAAATGGTCCTTAGCCAACAAGAAATGTTTGGCTGTGGT

Reverse complement sequence

ACCACAGCCAAACATTTCTTGTTGGCTAAGGACCATTTCTTTTGTTCAATGTCATACGACATGACGAGAGGAGCATTGTCCCTCTGTCTCTTTTGCCAGT[C/T]
AGCATCTGACTCATTTTCACCTCTGATAAGTTCAGCAGGTTCTATAGGACATGGGGTAGTCAACACCCAGTCCACCTCTCCCAAGATAAAAGCAAGGTCG

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 93.90% 4.10% 0.44% 1.52% NA
All Indica  2759 89.70% 7.00% 0.76% 2.61% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.40% 10.90% 0.67% 0.00% NA
Indica II  465 86.90% 0.60% 0.86% 11.61% NA
Indica III  913 91.70% 7.70% 0.44% 0.22% NA
Indica Intermediate  786 89.90% 6.90% 1.15% 2.04% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg1223507277 G -> DEL LOC_Os12g38280.1 N frameshift_variant Average:37.119; most accessible tissue: Minghui63 young leaf, score: 53.016 N N N N
vg1223507277 G -> A LOC_Os12g38280.1 missense_variant ; p.Asp113Asn; MODERATE nonsynonymous_codon ; D113N Average:37.119; most accessible tissue: Minghui63 young leaf, score: 53.016 unknown unknown TOLERATED 0.18

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1223507277 1.15E-06 2.59E-09 mr1038 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
vg1223507277 1.33E-06 5.86E-09 mr1038 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
vg1223507277 3.67E-06 NA mr1141 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
vg1223507277 2.79E-06 NA mr1141 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
vg1223507277 3.27E-07 1.25E-09 mr1389 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
vg1223507277 1.10E-06 1.90E-08 mr1389 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
vg1223507277 3.34E-07 1.20E-09 mr1038_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
vg1223507277 7.36E-07 1.47E-08 mr1038_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
vg1223507277 2.62E-10 1.30E-12 mr1389_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
vg1223507277 1.77E-09 1.37E-11 mr1389_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