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Detailed information for vg0826395442:

Variant ID: vg0826395442 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26395442
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATGGTTTTTTAAGCAACTTCTGTATGTAAACTTTTTGCAAAAAACATACCGTTTAGTAGTTTGAAAAGTGTACGTGCGGAAAACGAGTGAGAGGGGCTG[A/G]
GAAAAGGGGTGCCGAACAAAAATTCTCTAGGAGATATGAAAGCCACTGACATTTAGGTCCTACTCCACTCTTCTTTGAGCCCATATGCACGTTGCTGCTG

Reverse complement sequence

CAGCAGCAACGTGCATATGGGCTCAAAGAAGAGTGGAGTAGGACCTAAATGTCAGTGGCTTTCATATCTCCTAGAGAATTTTTGTTCGGCACCCCTTTTC[T/C]
CAGCCCCTCTCACTCGTTTTCCGCACGTACACTTTTCAAACTACTAAACGGTATGTTTTTTGCAAAAAGTTTACATACAGAAGTTGCTTAAAAAACCATA

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 89.60% 8.10% 2.26% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 68.50% 24.60% 6.94% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 42.10% 45.90% 11.99% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 87.60% 7.50% 4.98% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 10.00% 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
vg0826395442 A -> G LOC_Os08g41800.1 upstream_gene_variant ; 2882.0bp to feature; MODIFIER silent_mutation Average:83.17; most accessible tissue: Callus, score: 91.991 N N N N
vg0826395442 A -> G LOC_Os08g41790.1 downstream_gene_variant ; 153.0bp to feature; MODIFIER silent_mutation Average:83.17; most accessible tissue: Callus, score: 91.991 N N N N
vg0826395442 A -> G LOC_Os08g41790-LOC_Os08g41800 intergenic_region ; MODIFIER silent_mutation Average:83.17; most accessible tissue: Callus, score: 91.991 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)
vg0826395442 A G 0.0 0.01 0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826395442 NA 5.08E-07 mr1163 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
vg0826395442 NA 5.41E-06 mr1910 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
vg0826395442 NA 2.45E-08 mr1977 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
vg0826395442 NA 3.68E-09 mr1002_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
vg0826395442 NA 8.53E-23 mr1010_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
vg0826395442 NA 2.17E-12 mr1010_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
vg0826395442 NA 1.79E-11 mr1011_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
vg0826395442 NA 5.76E-08 mr1011_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
vg0826395442 4.23E-06 1.20E-15 mr1013_2 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
vg0826395442 NA 9.51E-08 mr1013_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
vg0826395442 NA 5.95E-06 mr1164_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
vg0826395442 NA 1.21E-07 mr1977_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