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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0306324522:

Variant ID: vg0306324522 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 6324522
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


GCGTTCACATCACCAGACGAGTAACTTTTTAACTCGGGACAAATGGGATGGGAAAAGCCTTTGCAGGCGGTGGTAGTAGTAAAAGCGGTCCATGAGGATG[C/T]
GGCACATGAGAAAGGCGAGAAATCCGAAGTTGGACCCAGAAAAAACTAAAAGCCAGGAAGGCGAGCGCTGAGAGGCGCGCTACTTCCTTCGTAGCGCCAC

Reverse complement sequence

GTGGCGCTACGAAGGAAGTAGCGCGCCTCTCAGCGCTCGCCTTCCTGGCTTTTAGTTTTTTCTGGGTCCAACTTCGGATTTCTCGCCTTTCTCATGTGCC[G/A]
CATCCTCATGGACCGCTTTTACTACTACCACCGCCTGCAAAGGCTTTTCCCATCCCATTTGTCCCGAGTTAAAAAGTTACTCGTCTGGTGATGTGAACGC

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 60.90% 36.50% 2.60% 0.00% NA
All Indica  2759 72.60% 27.40% 0.07% 0.00% NA
All Japonica  1512 30.80% 61.50% 7.67% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 61.00% 38.70% 0.34% 0.00% NA
Indica II  465 37.00% 63.00% 0.00% 0.00% NA
Indica III  913 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 71.60% 28.40% 0.00% 0.00% NA
Temperate Japonica  767 34.60% 54.60% 10.82% 0.00% NA
Tropical Japonica  504 30.00% 67.10% 2.98% 0.00% NA
Japonica Intermediate  241 20.70% 71.80% 7.47% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 55.60% 40.00% 4.44% 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
vg0306324522 C -> T LOC_Os03g12050.1 upstream_gene_variant ; 490.0bp to feature; MODIFIER silent_mutation Average:77.143; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0306324522 C -> T LOC_Os03g12064.1 upstream_gene_variant ; 2764.0bp to feature; MODIFIER silent_mutation Average:77.143; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0306324522 C -> T LOC_Os03g12064.2 upstream_gene_variant ; 2764.0bp to feature; MODIFIER silent_mutation Average:77.143; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0306324522 C -> T LOC_Os03g12064.3 upstream_gene_variant ; 2764.0bp to feature; MODIFIER silent_mutation Average:77.143; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0306324522 C -> T LOC_Os03g12064.6 upstream_gene_variant ; 2764.0bp to feature; MODIFIER silent_mutation Average:77.143; most accessible tissue: Minghui63 flower, score: 93.128 N N N N
vg0306324522 C -> T LOC_Os03g12050-LOC_Os03g12064 intergenic_region ; MODIFIER silent_mutation Average:77.143; most accessible tissue: Minghui63 flower, score: 93.128 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)
vg0306324522 C T -0.01 0.0 0.01 -0.02 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0306324522 NA 7.97E-18 Plant_height 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
vg0306324522 NA 2.36E-15 Plant_height Ind_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
vg0306324522 NA 3.21E-07 mr1060_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
vg0306324522 NA 3.67E-06 mr1115_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
vg0306324522 NA 7.93E-06 mr1175_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
vg0306324522 NA 8.52E-06 mr1186_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
vg0306324522 NA 2.91E-10 mr1195_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
vg0306324522 NA 4.07E-07 mr1268_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
vg0306324522 NA 1.46E-07 mr1349_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
vg0306324522 NA 1.24E-13 mr1352_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
vg0306324522 NA 2.14E-08 mr1358_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
vg0306324522 NA 8.12E-08 mr1358_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
vg0306324522 NA 4.21E-06 mr1359_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
vg0306324522 NA 1.63E-06 mr1378_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
vg0306324522 NA 1.54E-06 mr1428_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
vg0306324522 NA 1.43E-07 mr1478_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
vg0306324522 NA 4.15E-06 mr1511_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
vg0306324522 NA 2.40E-06 mr1520_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
vg0306324522 NA 2.83E-12 mr1546_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
vg0306324522 NA 5.32E-06 mr1576_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
vg0306324522 NA 2.89E-07 mr1582_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
vg0306324522 NA 9.56E-06 mr1654_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
vg0306324522 NA 1.17E-07 mr1743_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
vg0306324522 NA 4.16E-06 mr1761_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
vg0306324522 NA 6.83E-06 mr1836_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
vg0306324522 NA 9.16E-08 mr1850_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
vg0306324522 4.51E-06 4.51E-06 mr1958_2 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
vg0306324522 NA 6.89E-09 mr1971_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