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Detailed information for vg0141973334:

Variant ID: vg0141973334 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41973334
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAACAAAGAGAGTATAAATGTCATGGACTTCAATATAGATAGAATCGCCACCAGATCCTGGACTTCATTTAGATGAAATCATCCACGAAATCTCAAAA[C/T]
TGTATTAGTGCCACCGGATCCACGAATTGCATGCCACCGTGGAAGAAGTGCCGAAAAGTAGCAAGAGGATTGCGGCCAAGCTCGCGCTCGCCTGCCCGAG

Reverse complement sequence

CTCGGGCAGGCGAGCGCGAGCTTGGCCGCAATCCTCTTGCTACTTTTCGGCACTTCTTCCACGGTGGCATGCAATTCGTGGATCCGGTGGCACTAATACA[G/A]
TTTTGAGATTTCGTGGATGATTTCATCTAAATGAAGTCCAGGATCTGGTGGCGATTCTATCTATATTGAAGTCCATGACATTTATACTCTCTTTGTTTCA

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 89.80% 10.20% 0.00% 0.00% NA
All Indica  2759 85.00% 15.00% 0.00% 0.00% NA
All Japonica  1512 95.80% 4.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 81.50% 18.50% 0.00% 0.00% NA
Indica II  465 89.50% 10.50% 0.00% 0.00% NA
Indica III  913 87.10% 12.90% 0.00% 0.00% NA
Indica Intermediate  786 82.70% 17.30% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 87.90% 12.10% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0141973334 C -> T LOC_Os01g72370.1 3_prime_UTR_variant ; 2378.0bp to feature; MODIFIER silent_mutation Average:84.945; most accessible tissue: Zhenshan97 flag leaf, score: 98.323 N N N N
vg0141973334 C -> T LOC_Os01g72350.1 downstream_gene_variant ; 3190.0bp to feature; MODIFIER silent_mutation Average:84.945; most accessible tissue: Zhenshan97 flag leaf, score: 98.323 N N N N
vg0141973334 C -> T LOC_Os01g72360.1 downstream_gene_variant ; 311.0bp to feature; MODIFIER silent_mutation Average:84.945; most accessible tissue: Zhenshan97 flag leaf, score: 98.323 N N N N
vg0141973334 C -> T LOC_Os01g72350.2 downstream_gene_variant ; 3190.0bp to feature; MODIFIER silent_mutation Average:84.945; most accessible tissue: Zhenshan97 flag leaf, score: 98.323 N N N N
vg0141973334 C -> T LOC_Os01g72370.2 downstream_gene_variant ; 1844.0bp to feature; MODIFIER silent_mutation Average:84.945; most accessible tissue: Zhenshan97 flag leaf, score: 98.323 N N N N
vg0141973334 C -> T LOC_Os01g72370.3 intron_variant ; MODIFIER silent_mutation Average:84.945; most accessible tissue: Zhenshan97 flag leaf, score: 98.323 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)
vg0141973334 C T -0.03 -0.01 -0.03 -0.05 -0.07 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141973334 NA 3.30E-07 Spikelet_length 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
vg0141973334 NA 6.81E-07 mr1038 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
vg0141973334 NA 8.24E-07 mr1038 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
vg0141973334 NA 5.25E-10 mr1389 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
vg0141973334 NA 6.56E-09 mr1389 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
vg0141973334 NA 2.43E-13 mr1038_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
vg0141973334 NA 5.66E-12 mr1038_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
vg0141973334 NA 4.45E-06 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
vg0141973334 NA 7.72E-06 mr1236_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
vg0141973334 NA 1.86E-07 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
vg0141973334 NA 1.34E-10 mr1389_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
vg0141973334 NA 3.57E-10 mr1389_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
vg0141973334 NA 1.29E-06 mr1480_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
vg0141973334 NA 7.64E-06 mr1616_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
vg0141973334 NA 1.19E-08 mr1627_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
vg0141973334 6.33E-06 NA mr1669_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
vg0141973334 NA 6.97E-07 mr1669_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
vg0141973334 NA 4.97E-06 mr1706_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
vg0141973334 8.54E-06 2.96E-08 mr1749_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
vg0141973334 2.61E-06 1.75E-06 mr1768_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
vg0141973334 3.89E-06 3.89E-06 mr1821_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
vg0141973334 NA 2.79E-08 mr1968_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
vg0141973334 NA 6.40E-06 mr1974_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