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Detailed information for vg1211896931:

Variant ID: vg1211896931 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 11896931
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCCTTACATCCTCCTATTGGTACAATTTTATAGGGACGGGTAAGTGCATGATAGTAGTGATTAGTGGTACCGAAAGAATTGATACTTATGATGAAATC[A/G]
TCATCGACAATGTTAGGACACACGAAGCATCTTTGTCCTCAAGTTCGTTGCCTTACATACCTTATTACCTGACAACGGTCACCACAATGACACTCTGGAT

Reverse complement sequence

ATCCAGAGTGTCATTGTGGTGACCGTTGTCAGGTAATAAGGTATGTAAGGCAACGAACTTGAGGACAAAGATGCTTCGTGTGTCCTAACATTGTCGATGA[T/C]
GATTTCATCATAAGTATCAATTCTTTCGGTACCACTAATCACTACTATCATGCACTTACCCGTCCCTATAAAATTGTACCAATAGGAGGATGTAAGGAAT

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 57.50% 25.90% 0.23% 16.42% NA
All Indica  2759 76.80% 19.00% 0.11% 4.13% NA
All Japonica  1512 16.90% 44.20% 0.33% 38.62% NA
Aus  269 79.60% 0.00% 0.37% 20.07% NA
Indica I  595 53.10% 46.60% 0.00% 0.34% NA
Indica II  465 75.70% 9.70% 0.65% 13.98% NA
Indica III  913 90.60% 7.30% 0.00% 2.08% NA
Indica Intermediate  786 79.30% 17.20% 0.00% 3.56% NA
Temperate Japonica  767 10.30% 77.70% 0.26% 11.73% NA
Tropical Japonica  504 17.90% 2.60% 0.60% 78.97% NA
Japonica Intermediate  241 35.70% 24.50% 0.00% 39.83% NA
VI/Aromatic  96 85.40% 0.00% 1.04% 13.54% NA
Intermediate  90 53.30% 33.30% 1.11% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1211896931 A -> DEL N N silent_mutation Average:44.608; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 N N N N
vg1211896931 A -> G LOC_Os12g20370.1 upstream_gene_variant ; 1742.0bp to feature; MODIFIER silent_mutation Average:44.608; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 N N N N
vg1211896931 A -> G LOC_Os12g20380.1 upstream_gene_variant ; 3859.0bp to feature; MODIFIER silent_mutation Average:44.608; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 N N N N
vg1211896931 A -> G LOC_Os12g20370-LOC_Os12g20380 intergenic_region ; MODIFIER silent_mutation Average:44.608; most accessible tissue: Zhenshan97 flag leaf, score: 80.373 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1211896931 NA 3.32E-07 mr1002 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
vg1211896931 NA 1.75E-15 mr1023 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
vg1211896931 NA 3.41E-13 mr1079 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
vg1211896931 NA 1.79E-14 mr1142 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
vg1211896931 NA 4.38E-10 mr1178 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
vg1211896931 NA 1.34E-07 mr1186 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
vg1211896931 NA 1.47E-14 mr1489 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
vg1211896931 NA 1.52E-14 mr1491 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
vg1211896931 NA 1.60E-06 mr1606 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
vg1211896931 2.93E-06 1.62E-08 mr1639 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
vg1211896931 NA 4.03E-06 mr1657 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
vg1211896931 NA 1.44E-13 mr1778 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
vg1211896931 NA 1.54E-16 mr1023_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
vg1211896931 NA 1.03E-07 mr1031_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
vg1211896931 NA 1.13E-13 mr1079_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
vg1211896931 NA 4.50E-08 mr1189_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
vg1211896931 NA 6.65E-06 mr1263_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
vg1211896931 NA 1.82E-07 mr1308_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
vg1211896931 NA 1.83E-08 mr1338_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
vg1211896931 NA 6.75E-06 mr1346_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
vg1211896931 NA 8.73E-07 mr1361_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
vg1211896931 NA 3.45E-08 mr1378_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
vg1211896931 NA 2.70E-15 mr1489_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
vg1211896931 NA 1.51E-06 mr1745_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
vg1211896931 NA 7.69E-14 mr1778_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
vg1211896931 NA 8.42E-06 mr1864_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
vg1211896931 NA 2.53E-06 mr1966_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