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Detailed information for vg1210313817:

Variant ID: vg1210313817 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 10313817
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.61, A: 0.38, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:


AGAGTTCTGGATAGTAAGAATGAATAAAGGGAATGAAAGTAAGCAGTAAATACGTATGTAAACTATTGTAGCAAGTAAGGGTATGAAATCATAGAAATCA[G/A]
ATAGGGACAAAAGGAAACACGAATTATATCACCGAAGTTCGGATACAAAGATCTTACGTCTCTACTGTGGGACTCTAAAGAGCCAGATCACTTTTGATCC

Reverse complement sequence

GGATCAAAAGTGATCTGGCTCTTTAGAGTCCCACAGTAGAGACGTAAGATCTTTGTATCCGAACTTCGGTGATATAATTCGTGTTTCCTTTTGTCCCTAT[C/T]
TGATTTCTATGATTTCATACCCTTACTTGCTACAATAGTTTACATACGTATTTACTGCTTACTTTCATTCCCTTTATTCATTCTTACTATCCAGAACTCT

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 61.20% 38.40% 0.17% 0.25% NA
All Indica  2759 55.50% 44.00% 0.11% 0.33% NA
All Japonica  1512 72.10% 27.80% 0.07% 0.07% NA
Aus  269 50.90% 48.70% 0.37% 0.00% NA
Indica I  595 42.00% 57.60% 0.00% 0.34% NA
Indica II  465 60.00% 39.60% 0.00% 0.43% NA
Indica III  913 61.90% 37.60% 0.11% 0.44% NA
Indica Intermediate  786 55.70% 43.90% 0.25% 0.13% NA
Temperate Japonica  767 82.40% 17.50% 0.13% 0.00% NA
Tropical Japonica  504 64.30% 35.50% 0.00% 0.20% NA
Japonica Intermediate  241 55.60% 44.40% 0.00% 0.00% NA
VI/Aromatic  96 79.20% 19.80% 1.04% 0.00% NA
Intermediate  90 62.20% 33.30% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1210313817 G -> DEL N N silent_mutation Average:53.894; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N
vg1210313817 G -> A LOC_Os12g17940.1 upstream_gene_variant ; 2933.0bp to feature; MODIFIER silent_mutation Average:53.894; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N
vg1210313817 G -> A LOC_Os12g17940-LOC_Os12g17950 intergenic_region ; MODIFIER silent_mutation Average:53.894; most accessible tissue: Zhenshan97 young leaf, score: 79.783 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1210313817 NA 8.54E-10 mr1156 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
vg1210313817 NA 3.90E-09 mr1164 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
vg1210313817 NA 6.00E-06 mr1173 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
vg1210313817 NA 4.21E-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
vg1210313817 NA 9.31E-06 mr1192 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
vg1210313817 NA 6.87E-06 mr1245 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
vg1210313817 5.66E-06 5.66E-06 mr1258 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
vg1210313817 NA 1.41E-08 mr1280 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
vg1210313817 NA 3.11E-07 mr1289 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
vg1210313817 NA 1.14E-07 mr1318 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
vg1210313817 NA 9.29E-06 mr1507 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
vg1210313817 NA 6.33E-08 mr1729 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
vg1210313817 NA 4.11E-06 mr1788 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
vg1210313817 NA 3.55E-06 mr1810 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
vg1210313817 NA 3.27E-06 mr1851 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
vg1210313817 NA 6.72E-07 mr1164_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
vg1210313817 NA 7.11E-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