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Detailed information for vg1015531611:

Variant ID: vg1015531611 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 15531611
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCGGCGCCGGCGTCCTCGGCGGCGCGGCACAGCGCCTCCCGGGGCTCCCCCTCCACCGCCACCGTCGCCGCGGCCACCCCTCGCCGCTCGCAGACCAGC[T/C]
TCGCCCTGACGAGCAGGTTCCGCGCGTTCTCCGCCTGCGCCGCCCGCACCGCTTCCATCATCGACGCCGCGCCGTACACCGCCGACCCTGCGCGAACACC

Reverse complement sequence

GGTGTTCGCGCAGGGTCGGCGGTGTACGGCGCGGCGTCGATGATGGAAGCGGTGCGGGCGGCGCAGGCGGAGAACGCGCGGAACCTGCTCGTCAGGGCGA[A/G]
GCTGGTCTGCGAGCGGCGAGGGGTGGCCGCGGCGACGGTGGCGGTGGAGGGGGAGCCCCGGGAGGCGCTGTGCCGCGCCGCCGAGGACGCCGGCGCCGGC

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 87.60% 11.70% 0.68% 0.00% NA
All Indica  2759 99.50% 0.40% 0.04% 0.00% NA
All Japonica  1512 62.80% 35.30% 1.92% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 99.40% 0.40% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 32.30% 64.90% 2.74% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 84.20% 12.40% 3.32% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 86.70% 11.10% 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
vg1015531611 T -> C LOC_Os10g29900.1 downstream_gene_variant ; 58.0bp to feature; MODIFIER silent_mutation Average:80.981; most accessible tissue: Zhenshan97 young leaf, score: 90.078 N N N N
vg1015531611 T -> C LOC_Os10g29880-LOC_Os10g29900 intergenic_region ; MODIFIER silent_mutation Average:80.981; most accessible tissue: Zhenshan97 young leaf, score: 90.078 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)
vg1015531611 T C 0.03 0.02 0.03 0.03 0.05 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1015531611 NA 6.11E-13 Heading_date 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
vg1015531611 NA 9.20E-12 Heading_date Jap_All YES 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
vg1015531611 NA 5.12E-16 Spikelet_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
vg1015531611 NA 4.04E-07 mr1252_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
vg1015531611 NA 2.33E-08 mr1576_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
vg1015531611 NA 8.08E-08 mr1805_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