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Detailed information for vg0117162013:

Variant ID: vg0117162013 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 17162013
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.65, A: 0.35, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:


TGGCGGCTGCAGCTTGCTGCTGCCGTTGGTTGGAAGCATCCCACGGGATGGAAACGTTTGCGCGTGCTTTCCAATCGTTTTTTTGTGGGCAGCATGGGAA[T/A]
GCGTGCGTGCGAGTATTAGGCCCTGTTTAGATGAGACTAAAACTTTTAAGTCCCTATCACATCGGATGTTTGAAAATTAATTATAAATATTAAACGTAGA

Reverse complement sequence

TCTACGTTTAATATTTATAATTAATTTTCAAACATCCGATGTGATAGGGACTTAAAAGTTTTAGTCTCATCTAAACAGGGCCTAATACTCGCACGCACGC[A/T]
TTCCCATGCTGCCCACAAAAAAACGATTGGAAAGCACGCGCAAACGTTTCCATCCCGTGGGATGCTTCCAACCAACGGCAGCAGCAAGCTGCAGCCGCCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.80% 37.20% 0.06% 0.00% NA
All Indica  2759 97.60% 2.30% 0.11% 0.00% NA
All Japonica  1512 2.70% 97.30% 0.00% 0.00% NA
Aus  269 68.40% 31.60% 0.00% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 96.10% 3.70% 0.22% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 95.20% 4.70% 0.13% 0.00% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 5.40% 94.60% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 46.70% 53.30% 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
vg0117162013 T -> A LOC_Os01g31370.1 upstream_gene_variant ; 303.0bp to feature; MODIFIER silent_mutation Average:98.511; most accessible tissue: Zhenshan97 root, score: 99.61 N N N N
vg0117162013 T -> A LOC_Os01g31360.2 downstream_gene_variant ; 4157.0bp to feature; MODIFIER silent_mutation Average:98.511; most accessible tissue: Zhenshan97 root, score: 99.61 N N N N
vg0117162013 T -> A LOC_Os01g31380.1 downstream_gene_variant ; 4542.0bp to feature; MODIFIER silent_mutation Average:98.511; most accessible tissue: Zhenshan97 root, score: 99.61 N N N N
vg0117162013 T -> A LOC_Os01g31360.3 downstream_gene_variant ; 4168.0bp to feature; MODIFIER silent_mutation Average:98.511; most accessible tissue: Zhenshan97 root, score: 99.61 N N N N
vg0117162013 T -> A LOC_Os01g31360.5 downstream_gene_variant ; 4157.0bp to feature; MODIFIER silent_mutation Average:98.511; most accessible tissue: Zhenshan97 root, score: 99.61 N N N N
vg0117162013 T -> A LOC_Os01g31360.6 downstream_gene_variant ; 4157.0bp to feature; MODIFIER silent_mutation Average:98.511; most accessible tissue: Zhenshan97 root, score: 99.61 N N N N
vg0117162013 T -> A LOC_Os01g31360.4 downstream_gene_variant ; 4157.0bp to feature; MODIFIER silent_mutation Average:98.511; most accessible tissue: Zhenshan97 root, score: 99.61 N N N N
vg0117162013 T -> A LOC_Os01g31370-LOC_Os01g31380 intergenic_region ; MODIFIER silent_mutation Average:98.511; most accessible tissue: Zhenshan97 root, score: 99.61 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)
vg0117162013 T A 0.0 0.03 0.02 0.02 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0117162013 NA 9.70E-15 mr1164 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
vg0117162013 NA 2.38E-15 mr1228 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
vg0117162013 NA 1.18E-31 mr1298 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
vg0117162013 NA 6.35E-41 mr1509 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
vg0117162013 NA 5.89E-49 mr1519 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
vg0117162013 NA 3.27E-46 mr1558 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
vg0117162013 NA 4.34E-07 mr1680 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
vg0117162013 NA 4.34E-21 mr1698 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
vg0117162013 NA 6.44E-27 mr1731 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
vg0117162013 NA 2.66E-17 mr1825 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
vg0117162013 NA 5.25E-16 mr1040_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
vg0117162013 NA 2.11E-17 mr1281_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
vg0117162013 NA 1.15E-51 mr1519_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
vg0117162013 NA 5.98E-07 mr1568_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
vg0117162013 NA 1.49E-19 mr1581_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
vg0117162013 NA 3.78E-22 mr1609_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
vg0117162013 NA 2.21E-24 mr1708_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
vg0117162013 NA 4.37E-14 mr1770_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
vg0117162013 NA 1.07E-07 mr1783_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
vg0117162013 NA 1.35E-07 mr1804_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
vg0117162013 NA 6.67E-16 mr1836_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
vg0117162013 NA 1.09E-31 mr1841_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
vg0117162013 NA 2.82E-31 mr1913_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
vg0117162013 NA 2.86E-24 mr1916_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