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Detailed information for vg0827703459:

Variant ID: vg0827703459 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 27703459
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTCTTTTTCTCGATAAGAAGTGTAGAAGGCGCCAGGTCGCCGTAGTCTCGCTCGTCTCCGTGCATTCCGCGATCTCCGTGCCCGTCGACCACCGTGGTG[C/T]
TCGCCGGCGACGGACGGAGCGAGAATGCAGGGCGGATCTAGCGGCATCGTCTACGGCGGCCTCAAGTACCAGGCAAGCCTTCTCGAACCTTCTAGAACAG

Reverse complement sequence

CTGTTCTAGAAGGTTCGAGAAGGCTTGCCTGGTACTTGAGGCCGCCGTAGACGATGCCGCTAGATCCGCCCTGCATTCTCGCTCCGTCCGTCGCCGGCGA[G/A]
CACCACGGTGGTCGACGGGCACGGAGATCGCGGAATGCACGGAGACGAGCGAGACTACGGCGACCTGGCGCCTTCTACACTTCTTATCGAGAAAAAGAAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.20% 8.60% 0.19% 0.00% NA
All Indica  2759 99.90% 0.00% 0.04% 0.00% NA
All Japonica  1512 73.20% 26.40% 0.40% 0.00% NA
Aus  269 100.00% 0.00% 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 97.10% 2.60% 0.26% 0.00% NA
Tropical Japonica  504 30.20% 69.00% 0.79% 0.00% NA
Japonica Intermediate  241 87.10% 12.90% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 88.90% 8.90% 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
vg0827703459 C -> T LOC_Os08g44010.1 5_prime_UTR_variant ; 25.0bp to feature; MODIFIER silent_mutation Average:98.37; most accessible tissue: Zhenshan97 flower, score: 98.943 N N N N
vg0827703459 C -> T LOC_Os08g44010.2 5_prime_UTR_variant ; 25.0bp to feature; MODIFIER silent_mutation Average:98.37; most accessible tissue: Zhenshan97 flower, score: 98.943 N N N N
vg0827703459 C -> T LOC_Os08g44010.3 5_prime_UTR_variant ; 25.0bp to feature; MODIFIER silent_mutation Average:98.37; most accessible tissue: Zhenshan97 flower, score: 98.943 N N N N
vg0827703459 C -> T LOC_Os08g44010.4 5_prime_UTR_variant ; 25.0bp to feature; MODIFIER silent_mutation Average:98.37; most accessible tissue: Zhenshan97 flower, score: 98.943 N N N N
vg0827703459 C -> T LOC_Os08g44010.5 5_prime_UTR_variant ; 25.0bp to feature; MODIFIER silent_mutation Average:98.37; most accessible tissue: Zhenshan97 flower, score: 98.943 N N N N
vg0827703459 C -> T LOC_Os08g44000.1 upstream_gene_variant ; 3178.0bp to feature; MODIFIER silent_mutation Average:98.37; most accessible tissue: Zhenshan97 flower, score: 98.943 N N N N
vg0827703459 C -> T LOC_Os08g44015.1 upstream_gene_variant ; 4707.0bp to feature; MODIFIER silent_mutation Average:98.37; most accessible tissue: Zhenshan97 flower, score: 98.943 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)
vg0827703459 C T -0.01 -0.01 -0.02 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0827703459 NA 7.07E-13 Grain_width 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
vg0827703459 NA 2.39E-06 mr1364 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
vg0827703459 NA 8.08E-07 mr1382 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
vg0827703459 NA 2.90E-08 mr1382 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
vg0827703459 NA 1.36E-06 mr1388 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
vg0827703459 NA 1.73E-06 mr1398 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
vg0827703459 NA 2.83E-06 mr1398 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
vg0827703459 NA 1.28E-07 mr1551 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
vg0827703459 NA 3.93E-07 mr1554 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
vg0827703459 NA 5.82E-06 mr1600 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
vg0827703459 NA 1.35E-07 mr1602 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
vg0827703459 NA 4.81E-10 mr1696 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
vg0827703459 NA 7.43E-09 mr1696 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
vg0827703459 NA 9.66E-08 mr1916 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
vg0827703459 NA 8.19E-07 mr1121_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
vg0827703459 NA 5.63E-06 mr1211_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
vg0827703459 NA 2.94E-06 mr1243_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
vg0827703459 NA 3.24E-06 mr1295_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
vg0827703459 NA 1.60E-09 mr1543_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
vg0827703459 NA 9.91E-15 mr1742_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
vg0827703459 NA 9.63E-08 mr1786_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
vg0827703459 NA 1.42E-19 mr1871_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