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Detailed information for vg0433595407:

Variant ID: vg0433595407 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 33595407
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.03, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


TTGGCAAGATTCTTCCCCGAGGACCAGACATACCTCAGCACGGCATTTGCCGGCACACTGTAAGTACTGAAGAAAGTATAGTACTCAGCTCGCTTAACCC[G/A]
TAGCTAGCTAGCTCTGAACACCTGAGCCATGACAAGGTTGTAAATTTTGTTTCTGAAGAACTTTGTGATCCATGGATTTTCAGAGGCTACACGGCGCCTG

Reverse complement sequence

CAGGCGCCGTGTAGCCTCTGAAAATCCATGGATCACAAAGTTCTTCAGAAACAAAATTTACAACCTTGTCATGGCTCAGGTGTTCAGAGCTAGCTAGCTA[C/T]
GGGTTAAGCGAGCTGAGTACTATACTTTCTTCAGTACTTACAGTGTGCCGGCAAATGCCGTGCTGAGGTATGTCTGGTCCTCGGGGAAGAATCTTGCCAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.40% 43.90% 0.17% 0.59% NA
All Indica  2759 84.50% 14.50% 0.18% 0.91% NA
All Japonica  1512 16.50% 83.30% 0.07% 0.13% NA
Aus  269 0.40% 99.60% 0.00% 0.00% NA
Indica I  595 88.90% 9.90% 0.34% 0.84% NA
Indica II  465 91.00% 8.40% 0.22% 0.43% NA
Indica III  913 82.60% 16.40% 0.11% 0.88% NA
Indica Intermediate  786 79.40% 19.20% 0.13% 1.27% NA
Temperate Japonica  767 0.70% 99.20% 0.13% 0.00% NA
Tropical Japonica  504 45.80% 53.80% 0.00% 0.40% NA
Japonica Intermediate  241 5.80% 94.20% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 36.70% 60.00% 2.22% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0433595407 G -> DEL N N silent_mutation Average:72.509; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0433595407 G -> A LOC_Os04g56350.1 upstream_gene_variant ; 3566.0bp to feature; MODIFIER silent_mutation Average:72.509; most accessible tissue: Minghui63 panicle, score: 84.552 N N N N
vg0433595407 G -> A LOC_Os04g56360.1 intron_variant ; MODIFIER silent_mutation Average:72.509; most accessible tissue: Minghui63 panicle, score: 84.552 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)
vg0433595407 G A -0.02 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0433595407 NA 4.21E-06 mr1011 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
vg0433595407 NA 5.45E-14 mr1013 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
vg0433595407 NA 6.09E-14 mr1031 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
vg0433595407 NA 2.11E-13 mr1056 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
vg0433595407 NA 2.54E-10 mr1248 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
vg0433595407 NA 1.76E-06 mr1624 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
vg0433595407 NA 3.11E-06 mr1676 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
vg0433595407 NA 1.56E-08 mr1770 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
vg0433595407 NA 9.13E-07 mr1805 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
vg0433595407 NA 1.19E-14 mr1807 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
vg0433595407 NA 3.48E-06 mr1092_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
vg0433595407 NA 4.04E-17 mr1352_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
vg0433595407 NA 5.69E-25 mr1422_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
vg0433595407 NA 1.44E-07 mr1624_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
vg0433595407 1.46E-06 6.31E-08 mr1681_2 Ind_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
vg0433595407 NA 4.97E-06 mr1723_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
vg0433595407 NA 4.68E-15 mr1807_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