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Detailed information for vg0506864701:

Variant ID: vg0506864701 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6864701
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTCGGACACGGTCAACCTTGTTTCATGCTGGATGGGCCTAGCCCAACCTGTGCAACAGGATTATGAGCAGTTTTTTTTTTCTTCTCTTATTAGAATGA[G/A]
GAATAAGTTCTCCTGAGGTACCTCAACTTAACAACGTGATTTTTTTAAGGTCCCTTAGCCACAAAACCATAAATGTGTACTCCTAAACTCACACAAACCG

Reverse complement sequence

CGGTTTGTGTGAGTTTAGGAGTACACATTTATGGTTTTGTGGCTAAGGGACCTTAAAAAAATCACGTTGTTAAGTTGAGGTACCTCAGGAGAACTTATTC[C/T]
TCATTCTAATAAGAGAAGAAAAAAAAAACTGCTCATAATCCTGTTGCACAGGTTGGGCTAGGCCCATCCAGCATGAAACAAGGTTGACCGTGTCCGAGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 73.10% 26.80% 0.17% 0.00% NA
All Indica  2759 89.30% 10.70% 0.07% 0.00% NA
All Japonica  1512 49.30% 50.40% 0.26% 0.00% NA
Aus  269 71.00% 29.00% 0.00% 0.00% NA
Indica I  595 96.50% 3.40% 0.17% 0.00% NA
Indica II  465 81.10% 18.90% 0.00% 0.00% NA
Indica III  913 90.00% 10.00% 0.00% 0.00% NA
Indica Intermediate  786 87.80% 12.10% 0.13% 0.00% NA
Temperate Japonica  767 79.70% 19.80% 0.52% 0.00% NA
Tropical Japonica  504 11.50% 88.50% 0.00% 0.00% NA
Japonica Intermediate  241 32.00% 68.00% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 97.90% 1.04% 0.00% NA
Intermediate  90 57.80% 41.10% 1.11% 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
vg0506864701 G -> A LOC_Os05g12000.1 upstream_gene_variant ; 186.0bp to feature; MODIFIER silent_mutation Average:95.465; most accessible tissue: Callus, score: 97.435 N N N N
vg0506864701 G -> A LOC_Os05g12010.1 upstream_gene_variant ; 2457.0bp to feature; MODIFIER silent_mutation Average:95.465; most accessible tissue: Callus, score: 97.435 N N N N
vg0506864701 G -> A LOC_Os05g11990.1 downstream_gene_variant ; 2066.0bp to feature; MODIFIER silent_mutation Average:95.465; most accessible tissue: Callus, score: 97.435 N N N N
vg0506864701 G -> A LOC_Os05g11990.2 downstream_gene_variant ; 2066.0bp to feature; MODIFIER silent_mutation Average:95.465; most accessible tissue: Callus, score: 97.435 N N N N
vg0506864701 G -> A LOC_Os05g12000-LOC_Os05g12010 intergenic_region ; MODIFIER silent_mutation Average:95.465; most accessible tissue: Callus, score: 97.435 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)
vg0506864701 G A -0.04 -0.03 -0.02 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506864701 NA 2.30E-13 Grain_thickness 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
vg0506864701 5.23E-07 NA mr1039 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
vg0506864701 3.44E-09 1.66E-10 mr1039 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
vg0506864701 2.12E-08 2.20E-21 mr1593 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
vg0506864701 NA 4.94E-09 mr1593 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
vg0506864701 1.01E-08 2.01E-22 mr1593 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
vg0506864701 4.29E-07 NA mr1632 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
vg0506864701 7.99E-08 4.37E-13 mr1632 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
vg0506864701 5.48E-06 1.02E-10 mr1873 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
vg0506864701 4.89E-06 NA mr1039_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
vg0506864701 4.39E-09 2.41E-10 mr1039_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
vg0506864701 NA 2.34E-08 mr1195_2 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
vg0506864701 3.83E-06 3.12E-07 mr1514_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
vg0506864701 NA 5.82E-07 mr1551_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
vg0506864701 NA 1.51E-07 mr1582_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
vg0506864701 2.29E-06 5.28E-26 mr1593_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
vg0506864701 NA 5.88E-09 mr1593_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
vg0506864701 1.33E-07 7.60E-28 mr1593_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
vg0506864701 3.95E-09 NA mr1632_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
vg0506864701 6.98E-12 1.40E-15 mr1632_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
vg0506864701 NA 2.56E-06 mr1866_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
vg0506864701 NA 2.25E-07 mr1873_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