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Detailed information for vg1126461419:

Variant ID: vg1126461419 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26461419
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CAAATATTGAGTAAACTTCATTTGTGTAAAATTTAGGATTTAAAGAATAAAATTTATATAGGAAATAGGCTAAAATAGGGTTAAATAGCCGGCTAGCACT[G/A]
TTCATTAGCCCCCTAGGTGTTTGATTTGGTTCCTAGCCCTCCTCCTCCTCCTGCCCGTCCCATCTTCTCTGCCGCGCACGCCTGGCCGCCCCGAGCCCCG

Reverse complement sequence

CGGGGCTCGGGGCGGCCAGGCGTGCGCGGCAGAGAAGATGGGACGGGCAGGAGGAGGAGGAGGGCTAGGAACCAAATCAAACACCTAGGGGGCTAATGAA[C/T]
AGTGCTAGCCGGCTATTTAACCCTATTTTAGCCTATTTCCTATATAAATTTTATTCTTTAAATCCTAAATTTTACACAAATGAAGTTTACTCAATATTTG

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 98.00% 0.40% 0.21% 1.44% NA
All Indica  2759 98.90% 0.10% 0.07% 0.94% NA
All Japonica  1512 95.70% 1.10% 0.46% 2.78% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.00% 0.17% NA
Indica II  465 94.60% 0.00% 0.22% 5.16% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.10% 0.13% 0.13% NA
Temperate Japonica  767 98.60% 0.40% 0.00% 1.04% NA
Tropical Japonica  504 92.50% 0.60% 0.40% 6.55% NA
Japonica Intermediate  241 93.40% 4.10% 2.07% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg1126461419 G -> A LOC_Os11g43810.1 upstream_gene_variant ; 3319.0bp to feature; MODIFIER silent_mutation Average:84.725; most accessible tissue: Zhenshan97 young leaf, score: 95.273 N N N N
vg1126461419 G -> A LOC_Os11g43800.1 downstream_gene_variant ; 1348.0bp to feature; MODIFIER silent_mutation Average:84.725; most accessible tissue: Zhenshan97 young leaf, score: 95.273 N N N N
vg1126461419 G -> A LOC_Os11g43800-LOC_Os11g43810 intergenic_region ; MODIFIER silent_mutation Average:84.725; most accessible tissue: Zhenshan97 young leaf, score: 95.273 N N N N
vg1126461419 G -> DEL N N silent_mutation Average:84.725; most accessible tissue: Zhenshan97 young leaf, score: 95.273 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg1126461419 G A -0.06 -0.04 -0.08 -0.04 -0.04 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126461419 NA 8.56E-06 mr1113 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
vg1126461419 NA 4.08E-06 mr1114 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
vg1126461419 2.71E-06 4.68E-09 mr1117 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
vg1126461419 NA 1.16E-06 mr1118 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
vg1126461419 8.15E-06 6.51E-08 mr1119 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
vg1126461419 NA 4.83E-06 mr1120 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
vg1126461419 1.28E-07 7.04E-10 mr1123 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
vg1126461419 NA 1.72E-06 mr1240 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
vg1126461419 3.81E-06 2.95E-10 mr1242 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
vg1126461419 4.46E-08 4.44E-11 mr1247 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
vg1126461419 7.25E-06 1.16E-08 mr1496 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
vg1126461419 2.20E-06 NA mr1614 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
vg1126461419 NA 3.18E-06 mr1736 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
vg1126461419 NA 3.38E-07 mr1917 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
vg1126461419 NA 1.71E-06 mr1936 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
vg1126461419 1.75E-06 4.83E-09 mr1113_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
vg1126461419 2.12E-07 7.84E-11 mr1114_2 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
vg1126461419 1.29E-07 7.11E-11 mr1117_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
vg1126461419 1.40E-06 2.74E-10 mr1118_2 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
vg1126461419 1.23E-07 7.14E-11 mr1119_2 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
vg1126461419 8.53E-08 1.04E-10 mr1120_2 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
vg1126461419 3.14E-08 1.40E-11 mr1123_2 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
vg1126461419 1.69E-08 9.39E-13 mr1240_2 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
vg1126461419 3.62E-08 5.67E-12 mr1242_2 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
vg1126461419 8.34E-08 3.65E-11 mr1247_2 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
vg1126461419 NA 1.43E-07 mr1495_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
vg1126461419 2.36E-07 5.52E-11 mr1496_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
vg1126461419 NA 2.78E-06 mr1691_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
vg1126461419 1.50E-06 6.13E-09 mr1936_2 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