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Detailed information for vg0420699382:

Variant ID: vg0420699382 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 20699382
Reference Allele: CAlternative Allele: T,A
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.58, T: 0.42, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTACCTTGTTAGATACAGAGTACCCCCTCCATCCCAAAAAAGACCAATCCTACCTACAAACCTGGATATGTGTGTGTCCAGATTTGTAGCTAGGAATT[C/T,A]
AGTTTTTTTGGATGGAGTAGTATAATCTTAACTTGATTAGTTACGGCATGTTATGTGTGGTGCATGCATGTGCACATTGAGTACGTTTTTGTTTAGCGAA

Reverse complement sequence

TTCGCTAAACAAAAACGTACTCAATGTGCACATGCATGCACCACACATAACATGCCGTAACTAATCAAGTTAAGATTATACTACTCCATCCAAAAAAACT[G/A,T]
AATTCCTAGCTACAAATCTGGACACACACATATCCAGGTTTGTAGGTAGGATTGGTCTTTTTTGGGATGGAGGGGGTACTCTGTATCTAACAAGGTACAC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.60% 27.90% 0.28% 0.00% A: 0.30%
All Indica  2759 97.50% 1.90% 0.11% 0.00% A: 0.51%
All Japonica  1512 19.40% 80.00% 0.66% 0.00% NA
Aus  269 92.60% 7.40% 0.00% 0.00% NA
Indica I  595 98.70% 0.80% 0.50% 0.00% NA
Indica II  465 94.00% 4.30% 0.00% 0.00% A: 1.72%
Indica III  913 99.30% 0.20% 0.00% 0.00% A: 0.44%
Indica Intermediate  786 96.60% 3.20% 0.00% 0.00% A: 0.25%
Temperate Japonica  767 7.30% 92.20% 0.52% 0.00% NA
Tropical Japonica  504 36.50% 63.10% 0.40% 0.00% NA
Japonica Intermediate  241 22.00% 76.30% 1.66% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 0.00% 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
vg0420699382 C -> A LOC_Os04g34160.1 upstream_gene_variant ; 3111.0bp to feature; MODIFIER silent_mutation Average:86.597; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg0420699382 C -> A LOC_Os04g34150.1 downstream_gene_variant ; 87.0bp to feature; MODIFIER silent_mutation Average:86.597; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg0420699382 C -> A LOC_Os04g34150-LOC_Os04g34160 intergenic_region ; MODIFIER silent_mutation Average:86.597; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg0420699382 C -> T LOC_Os04g34160.1 upstream_gene_variant ; 3111.0bp to feature; MODIFIER silent_mutation Average:86.597; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg0420699382 C -> T LOC_Os04g34150.1 downstream_gene_variant ; 87.0bp to feature; MODIFIER silent_mutation Average:86.597; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg0420699382 C -> T LOC_Os04g34150-LOC_Os04g34160 intergenic_region ; MODIFIER silent_mutation Average:86.597; most accessible tissue: Zhenshan97 panicle, score: 92.66 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)
vg0420699382 C A -0.01 -0.02 -0.03 0.01 -0.02 -0.04
vg0420699382 C T -0.02 -0.03 -0.03 0.0 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0420699382 NA 2.12E-11 Grain_weight All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0420699382 1.34E-06 NA mr1883 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
vg0420699382 1.86E-07 1.86E-07 mr1883 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
vg0420699382 NA 2.91E-33 mr1137_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
vg0420699382 NA 6.00E-12 mr1377_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
vg0420699382 NA 2.81E-06 mr1555_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
vg0420699382 NA 8.38E-28 mr1617_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
vg0420699382 NA 1.99E-07 mr1837_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