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Detailed information for vg0419219689:

Variant ID: vg0419219689 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 19219689
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAACAACACTTCGGTAATTTTGTATCTTTAATTTTGAAATCCCTCTTTCCGTCACTGGTGTCCATGCTCATACAGTCATACTGATCCCAATTCCCATAC[T/C]
GTGCTTCTCGTATGTAGGGAGAAAATGGTTAACAAACTTTATTTATATTGTTCCAAAATAAACTTTCTTTATATATACTACTACTACCGTATATTAATCG

Reverse complement sequence

CGATTAATATACGGTAGTAGTAGTATATATAAAGAAAGTTTATTTTGGAACAATATAAATAAAGTTTGTTAACCATTTTCTCCCTACATACGAGAAGCAC[A/G]
GTATGGGAATTGGGATCAGTATGACTGTATGAGCATGGACACCAGTGACGGAAAGAGGGATTTCAAAATTAAAGATACAAAATTACCGAAGTGTTGTTCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 34.60% 13.60% 4.00% 47.80% NA
All Indica  2759 15.80% 3.60% 5.40% 75.21% NA
All Japonica  1512 64.70% 34.80% 0.26% 0.20% NA
Aus  269 28.30% 1.50% 12.27% 57.99% NA
Indica I  595 19.70% 4.70% 0.50% 75.13% NA
Indica II  465 37.40% 6.20% 3.87% 52.47% NA
Indica III  913 1.20% 1.40% 10.19% 87.19% NA
Indica Intermediate  786 17.00% 3.70% 4.45% 74.81% NA
Temperate Japonica  767 37.40% 62.10% 0.26% 0.26% NA
Tropical Japonica  504 98.40% 1.40% 0.20% 0.00% NA
Japonica Intermediate  241 81.30% 17.80% 0.41% 0.41% NA
VI/Aromatic  96 94.80% 0.00% 2.08% 3.12% NA
Intermediate  90 56.70% 17.80% 1.11% 24.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0419219689 T -> C LOC_Os04g32050.1 upstream_gene_variant ; 1115.0bp to feature; MODIFIER silent_mutation Average:90.084; most accessible tissue: Zhenshan97 root, score: 96.5 N N N N
vg0419219689 T -> C LOC_Os04g32050.2 upstream_gene_variant ; 1115.0bp to feature; MODIFIER silent_mutation Average:90.084; most accessible tissue: Zhenshan97 root, score: 96.5 N N N N
vg0419219689 T -> C LOC_Os04g32030-LOC_Os04g32050 intergenic_region ; MODIFIER silent_mutation Average:90.084; most accessible tissue: Zhenshan97 root, score: 96.5 N N N N
vg0419219689 T -> DEL N N silent_mutation Average:90.084; most accessible tissue: Zhenshan97 root, score: 96.5 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)
vg0419219689 T C 0.0 0.0 -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
vg0419219689 NA 6.88E-12 Plant_height Jap_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
vg0419219689 NA 6.71E-13 Spikelet_length Jap_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
vg0419219689 NA 6.15E-06 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
vg0419219689 NA 1.27E-06 mr1324 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
vg0419219689 5.94E-09 6.34E-12 mr1405 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
vg0419219689 2.72E-10 1.13E-20 mr1521 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
vg0419219689 7.78E-08 7.78E-08 mr1521 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
vg0419219689 NA 1.10E-06 mr1521 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
vg0419219689 NA 2.68E-08 mr1549 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
vg0419219689 NA 3.55E-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
vg0419219689 2.74E-31 1.85E-40 mr1851 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
vg0419219689 1.51E-18 7.69E-21 mr1851 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
vg0419219689 4.35E-09 4.58E-13 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
vg0419219689 5.24E-29 1.23E-44 mr1864 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
vg0419219689 1.08E-17 1.90E-21 mr1864 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
vg0419219689 3.69E-10 1.69E-17 mr1864 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
vg0419219689 NA 1.11E-06 mr1170_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
vg0419219689 NA 3.14E-07 mr1310_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
vg0419219689 NA 3.24E-07 mr1405_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
vg0419219689 NA 7.15E-10 mr1486_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
vg0419219689 2.25E-09 1.98E-23 mr1521_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
vg0419219689 1.14E-06 1.77E-07 mr1521_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
vg0419219689 NA 2.09E-11 mr1521_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
vg0419219689 NA 2.30E-06 mr1588_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
vg0419219689 1.83E-10 2.11E-19 mr1851_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
vg0419219689 7.12E-06 NA mr1851_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
vg0419219689 NA 2.35E-06 mr1851_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
vg0419219689 6.08E-09 2.95E-22 mr1864_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
vg0419219689 NA 8.37E-10 mr1864_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
vg0419219689 NA 1.02E-06 mr1966_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