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Detailed information for vg0816338452:

Variant ID: vg0816338452 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 16338452
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAAGGAAAGGACTAAAGAGCGGAAAGATGGGAGGAAGAATATGGGACTTATATATAGGTAGGTCCCACCTTTTTTTTACTATGATGCCATGTAGGCGTCA[T/C]
ATTGCATACCCAGTCAACGTGCCATGTAGGACGAAACCACCATTCAAACCGCTCGAGTTAAATTGATCCGGTTTTCGTAGTTAAGGAGTCTCTATACCCG

Reverse complement sequence

CGGGTATAGAGACTCCTTAACTACGAAAACCGGATCAATTTAACTCGAGCGGTTTGAATGGTGGTTTCGTCCTACATGGCACGTTGACTGGGTATGCAAT[A/G]
TGACGCCTACATGGCATCATAGTAAAAAAAAGGTGGGACCTACCTATATATAAGTCCCATATTCTTCCTCCCATCTTTCCGCTCTTTAGTCCTTTCCTTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.10% 10.90% 1.02% 0.00% NA
All Indica  2759 96.80% 2.80% 0.43% 0.00% NA
All Japonica  1512 80.40% 17.20% 2.38% 0.00% NA
Aus  269 68.80% 31.20% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 93.30% 5.50% 1.20% 0.00% NA
Indica Intermediate  786 98.00% 2.00% 0.00% 0.00% NA
Temperate Japonica  767 67.10% 28.70% 4.17% 0.00% NA
Tropical Japonica  504 98.40% 1.40% 0.20% 0.00% NA
Japonica Intermediate  241 85.10% 13.70% 1.24% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0816338452 T -> C LOC_Os08g26850.1 upstream_gene_variant ; 4775.0bp to feature; MODIFIER silent_mutation Average:95.47; most accessible tissue: Zhenshan97 young leaf, score: 98.942 N N N N
vg0816338452 T -> C LOC_Os08g26870.1 downstream_gene_variant ; 1881.0bp to feature; MODIFIER silent_mutation Average:95.47; most accessible tissue: Zhenshan97 young leaf, score: 98.942 N N N N
vg0816338452 T -> C LOC_Os08g26870.2 downstream_gene_variant ; 1881.0bp to feature; MODIFIER silent_mutation Average:95.47; most accessible tissue: Zhenshan97 young leaf, score: 98.942 N N N N
vg0816338452 T -> C LOC_Os08g26870.3 downstream_gene_variant ; 1881.0bp to feature; MODIFIER silent_mutation Average:95.47; most accessible tissue: Zhenshan97 young leaf, score: 98.942 N N N N
vg0816338452 T -> C LOC_Os08g26870.4 downstream_gene_variant ; 1881.0bp to feature; MODIFIER silent_mutation Average:95.47; most accessible tissue: Zhenshan97 young leaf, score: 98.942 N N N N
vg0816338452 T -> C LOC_Os08g26870.5 downstream_gene_variant ; 1881.0bp to feature; MODIFIER silent_mutation Average:95.47; most accessible tissue: Zhenshan97 young leaf, score: 98.942 N N N N
vg0816338452 T -> C LOC_Os08g26860.1 intron_variant ; MODIFIER silent_mutation Average:95.47; most accessible tissue: Zhenshan97 young leaf, score: 98.942 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)
vg0816338452 T C 0.03 0.03 0.03 0.03 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0816338452 NA 6.94E-19 Awn_length 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
vg0816338452 NA 9.37E-07 mr1006 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
vg0816338452 NA 8.13E-07 mr1052 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
vg0816338452 6.41E-06 NA mr1157 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
vg0816338452 NA 6.23E-07 mr1126_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
vg0816338452 NA 5.72E-07 mr1567_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