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Detailed information for vg1015010372:

Variant ID: vg1015010372 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15010372
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCGCGGCAACTGCTCAAGTTCGACGAGCTCGCCTCCTCCCTCGCGGAGCTCATCGTTGGGCCCTGCTGTCGCCGTCGAGCAGGCAGAGCTCACTGAGCT[G/A]
TCCCTATAAGCATTTCTCACGGAATTCTTTGAGCAAAGAGAAAGAAGTTAACTAAGCTATCTGTTTTTTTTCTTCCGAAAGACCTCACATGCATGTATGG

Reverse complement sequence

CCATACATGCATGTGAGGTCTTTCGGAAGAAAAAAAACAGATAGCTTAGTTAACTTCTTTCTCTTTGCTCAAAGAATTCCGTGAGAAATGCTTATAGGGA[C/T]
AGCTCAGTGAGCTCTGCCTGCTCGACGGCGACAGCAGGGCCCAACGATGAGCTCCGCGAGGGAGGAGGCGAGCTCGTCGAACTTGAGCAGTTGCCGCGCG

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 63.40% 36.30% 0.30% 0.00% NA
All Indica  2759 96.90% 2.70% 0.43% 0.00% NA
All Japonica  1512 0.80% 99.20% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.00% 3.40% 0.67% 0.00% NA
Indica II  465 94.40% 4.90% 0.65% 0.00% NA
Indica III  913 99.80% 0.10% 0.11% 0.00% NA
Indica Intermediate  786 95.70% 3.80% 0.51% 0.00% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.80% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 44.40% 53.30% 2.22% 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
vg1015010372 G -> A LOC_Os10g28770.1 upstream_gene_variant ; 3092.0bp to feature; MODIFIER silent_mutation Average:80.712; most accessible tissue: Zhenshan97 flag leaf, score: 86.342 N N N N
vg1015010372 G -> A LOC_Os10g28780.1 downstream_gene_variant ; 294.0bp to feature; MODIFIER silent_mutation Average:80.712; most accessible tissue: Zhenshan97 flag leaf, score: 86.342 N N N N
vg1015010372 G -> A LOC_Os10g28770-LOC_Os10g28780 intergenic_region ; MODIFIER silent_mutation Average:80.712; most accessible tissue: Zhenshan97 flag leaf, score: 86.342 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)
vg1015010372 G A -0.04 -0.03 -0.04 -0.02 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015010372 1.64E-06 5.61E-06 mr1008 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
vg1015010372 5.64E-06 NA mr1009 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
vg1015010372 NA 2.04E-66 mr1027 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
vg1015010372 NA 2.48E-42 mr1591 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
vg1015010372 NA 1.50E-58 mr1594 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
vg1015010372 NA 4.99E-39 mr1645 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
vg1015010372 5.04E-06 6.86E-06 mr1758 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
vg1015010372 NA 8.46E-42 mr1891 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
vg1015010372 NA 4.61E-15 mr1933 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
vg1015010372 NA 6.45E-20 mr1362_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
vg1015010372 NA 8.02E-08 mr1645_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
vg1015010372 NA 1.17E-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