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Detailed information for vg1125519768:

Variant ID: vg1125519768 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25519768
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.70, A: 0.32, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:


CCGTCCTCCGCCACCACGCCTCCCTTCCCGCGCCTCCCCTCTCGCCCCTGCCGGATCTGACGGGATGGCGCCGCCGCCCCTGCCAGGCCGGCGCCGGCGC[A/C]
GCCGCTACACGCAGAGAAATGGAGAAAGGGAGAGAGAACTCGAGAGAAATGGAGAAAGAGAGAGAGGACAACCTTATCTCTTCTGAGTGTGGGCCCCGCC

Reverse complement sequence

GGCGGGGCCCACACTCAGAAGAGATAAGGTTGTCCTCTCTCTCTTTCTCCATTTCTCTCGAGTTCTCTCTCCCTTTCTCCATTTCTCTGCGTGTAGCGGC[T/G]
GCGCCGGCGCCGGCCTGGCAGGGGCGGCGGCGCCATCCCGTCAGATCCGGCAGGGGCGAGAGGGGAGGCGCGGGAAGGGAGGCGTGGTGGCGGAGGACGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 50.60% 12.20% 0.99% 36.25% NA
All Indica  2759 32.00% 14.10% 1.01% 52.85% NA
All Japonica  1512 84.70% 2.60% 0.33% 12.30% NA
Aus  269 52.40% 28.30% 4.46% 14.87% NA
Indica I  595 54.60% 32.10% 1.34% 11.93% NA
Indica II  465 58.30% 18.70% 0.86% 22.15% NA
Indica III  913 4.60% 4.20% 1.20% 90.03% NA
Indica Intermediate  786 31.20% 9.40% 0.64% 58.78% NA
Temperate Japonica  767 94.90% 2.30% 0.13% 2.61% NA
Tropical Japonica  504 69.00% 3.20% 0.79% 26.98% NA
Japonica Intermediate  241 85.10% 2.50% 0.00% 12.45% NA
VI/Aromatic  96 44.80% 55.20% 0.00% 0.00% NA
Intermediate  90 46.70% 18.90% 2.22% 32.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125519768 A -> DEL LOC_Os11g42400.1 N frameshift_variant Average:43.56; most accessible tissue: Zhenshan97 panicle, score: 88.35 N N N N
vg1125519768 A -> C LOC_Os11g42400.1 synonymous_variant ; p.Ala162Ala; LOW synonymous_codon Average:43.56; most accessible tissue: Zhenshan97 panicle, score: 88.35 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)
vg1125519768 A C -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125519768 NA 4.83E-06 mr1094 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
vg1125519768 1.29E-33 1.27E-51 mr1191 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
vg1125519768 1.02E-25 5.93E-36 mr1191 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
vg1125519768 7.73E-07 7.73E-07 mr1191 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
vg1125519768 NA 1.13E-06 mr1380 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
vg1125519768 NA 1.95E-09 mr1561 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
vg1125519768 6.00E-50 1.39E-74 mr1644 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
vg1125519768 1.22E-41 1.12E-56 mr1644 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
vg1125519768 1.91E-07 1.91E-07 mr1644 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
vg1125519768 NA 7.86E-07 mr1875 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
vg1125519768 NA 6.84E-07 mr1908 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
vg1125519768 NA 7.93E-06 mr1913 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
vg1125519768 NA 9.73E-06 mr1937 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
vg1125519768 3.80E-43 1.05E-69 mr1191_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
vg1125519768 6.78E-34 2.13E-52 mr1191_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
vg1125519768 1.07E-07 1.07E-07 mr1191_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
vg1125519768 NA 1.43E-06 mr1380_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
vg1125519768 NA 2.98E-07 mr1561_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
vg1125519768 NA 7.49E-07 mr1875_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
vg1125519768 NA 4.56E-07 mr1908_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
vg1125519768 NA 1.50E-06 mr1996_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