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Detailed information for vg1202073188:

Variant ID: vg1202073188 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 2073188
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCTGGGTCACGTCATTACTGCTCAAGGTGTGGCAGTGGATCCGTCGAATGTGGAGTCAGTTACTAAGTGGACCCCACCAAAGACAATTTTTCAGATCC[G/A]
GAGTTTTCTTGGACTTGCGGGTTATTACCGTCGGTTCATCGAAAATTTCTCTAAGATTGCCAGACCCATGACTCAGTTGCTGAAGAAAGATGAAAATTTT

Reverse complement sequence

AAAATTTTCATCTTTCTTCAGCAACTGAGTCATGGGTCTGGCAATCTTAGAGAAATTTTCGATGAACCGACGGTAATAACCCGCAAGTCCAAGAAAACTC[C/T]
GGATCTGAAAAATTGTCTTTGGTGGGGTCCACTTAGTAACTGACTCCACATTCGACGGATCCACTGCCACACCTTGAGCAGTAATGACGTGACCCAGAAA

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 50.40% 0.80% 2.41% 46.36% NA
All Indica  2759 17.60% 1.40% 4.02% 76.95% NA
All Japonica  1512 97.90% 0.00% 0.07% 1.98% NA
Aus  269 94.40% 0.00% 0.37% 5.20% NA
Indica I  595 21.20% 1.20% 3.87% 73.78% NA
Indica II  465 15.90% 2.20% 9.46% 72.47% NA
Indica III  913 11.60% 1.10% 1.64% 85.65% NA
Indica Intermediate  786 22.80% 1.70% 3.69% 71.88% NA
Temperate Japonica  767 96.70% 0.00% 0.13% 3.13% NA
Tropical Japonica  504 99.00% 0.00% 0.00% 0.99% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 97.90% 0.00% 1.04% 1.04% NA
Intermediate  90 74.40% 0.00% 0.00% 25.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1202073188 G -> DEL LOC_Os12g04830.1 N frameshift_variant Average:10.868; most accessible tissue: Callus, score: 31.634 N N N N
vg1202073188 G -> A LOC_Os12g04830.1 missense_variant ; p.Arg867Gln; MODERATE stop_gained Average:10.868; most accessible tissue: Callus, score: 31.634 N N N N
vg1202073188 G -> A LOC_Os12g04830.1 missense_variant ; p.Arg867Gln; MODERATE nonsynonymous_codon ; R867Q Average:10.868; most accessible tissue: Callus, score: 31.634 unknown unknown DELETERIOUS 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1202073188 NA 2.99E-08 mr1109 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
vg1202073188 NA 6.37E-08 mr1129 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
vg1202073188 2.00E-07 1.67E-23 mr1255 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
vg1202073188 1.67E-06 2.62E-10 mr1255 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
vg1202073188 NA 6.83E-08 mr1257 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
vg1202073188 NA 3.57E-06 mr1435 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
vg1202073188 NA 1.71E-07 mr1129_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
vg1202073188 NA 9.88E-09 mr1236_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
vg1202073188 NA 3.00E-08 mr1236_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
vg1202073188 NA 5.01E-06 mr1255_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
vg1202073188 NA 5.80E-07 mr1257_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