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Detailed information for vg0405535133:

Variant ID: vg0405535133 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5535133
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTTGTTGACGTCCCCGAGCGGGATTATAGCCGGCCAGAGCTAGTCGACGGCGGTCTTCGTTCCCTCGGACTCAAAACATAAGAGCACCGCCTTGGACT[A/T]
CTTGGTGCCTAGTCCCAAGCTCCCAGCGTGAGTGTGTGCCACGCCTGGTGTGCTAGGATGGTGAAGCTGGTGGGCATGTATGCCATGGTCGACGGGAACA

Reverse complement sequence

TGTTCCCGTCGACCATGGCATACATGCCCACCAGCTTCACCATCCTAGCACACCAGGCGTGGCACACACTCACGCTGGGAGCTTGGGACTAGGCACCAAG[T/A]
AGTCCAAGGCGGTGCTCTTATGTTTTGAGTCCGAGGGAACGAAGACCGCCGTCGACTAGCTCTGGCCGGCTATAATCCCGCTCGGGGACGTCAACAAGAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.20% 25.60% 0.00% 0.19% NA
All Indica  2759 93.20% 6.50% 0.00% 0.33% NA
All Japonica  1512 33.50% 66.50% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 95.60% 4.00% 0.00% 0.34% NA
Indica II  465 89.50% 10.10% 0.00% 0.43% NA
Indica III  913 96.30% 3.40% 0.00% 0.33% NA
Indica Intermediate  786 89.90% 9.80% 0.00% 0.25% NA
Temperate Japonica  767 34.90% 65.10% 0.00% 0.00% NA
Tropical Japonica  504 37.50% 62.50% 0.00% 0.00% NA
Japonica Intermediate  241 20.30% 79.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0405535133 A -> DEL N N silent_mutation Average:85.671; most accessible tissue: Minghui63 flag leaf, score: 96.485 N N N N
vg0405535133 A -> T LOC_Os04g10240.1 upstream_gene_variant ; 4787.0bp to feature; MODIFIER silent_mutation Average:85.671; most accessible tissue: Minghui63 flag leaf, score: 96.485 N N N N
vg0405535133 A -> T LOC_Os04g10240.2 upstream_gene_variant ; 4787.0bp to feature; MODIFIER silent_mutation Average:85.671; most accessible tissue: Minghui63 flag leaf, score: 96.485 N N N N
vg0405535133 A -> T LOC_Os04g10260.1 downstream_gene_variant ; 4441.0bp to feature; MODIFIER silent_mutation Average:85.671; most accessible tissue: Minghui63 flag leaf, score: 96.485 N N N N
vg0405535133 A -> T LOC_Os04g10250.1 intron_variant ; MODIFIER silent_mutation Average:85.671; most accessible tissue: Minghui63 flag leaf, score: 96.485 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)
vg0405535133 A T -0.06 -0.05 -0.03 -0.08 -0.06 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405535133 2.49E-14 6.19E-30 mr1035 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
vg0405535133 6.71E-06 1.24E-07 mr1035 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
vg0405535133 3.82E-08 3.22E-11 mr1035 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
vg0405535133 1.46E-12 6.38E-28 mr1062 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
vg0405535133 6.11E-07 1.35E-10 mr1062 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
vg0405535133 5.71E-14 2.80E-08 mr1525 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
vg0405535133 9.83E-06 NA mr1525 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
vg0405535133 1.15E-09 1.15E-09 mr1525 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
vg0405535133 1.28E-13 1.68E-26 mr1626 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
vg0405535133 NA 1.25E-06 mr1626 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
vg0405535133 1.36E-08 4.96E-12 mr1626 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
vg0405535133 1.04E-11 2.21E-37 mr1631 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
vg0405535133 NA 1.83E-06 mr1631 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
vg0405535133 6.31E-09 6.31E-09 mr1631 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
vg0405535133 6.60E-19 1.54E-31 mr1035_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
vg0405535133 1.57E-09 2.60E-13 mr1035_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
vg0405535133 3.02E-17 2.45E-35 mr1062_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
vg0405535133 1.83E-07 2.96E-07 mr1062_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
vg0405535133 9.13E-10 4.68E-13 mr1062_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
vg0405535133 1.39E-08 1.43E-08 mr1525_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
vg0405535133 1.17E-07 3.16E-07 mr1525_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
vg0405535133 2.89E-10 2.89E-10 mr1525_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
vg0405535133 5.84E-18 1.38E-49 mr1631_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
vg0405535133 3.20E-09 1.78E-14 mr1631_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