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Detailed information for vg0919588048:

Variant ID: vg0919588048 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 19588048
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTATAGTCATCCCCCGCACGCGATTTTTCTCCCTTACAACTTACACGAATCATAGGGTCTGTTTGGTAAAGCTCCAACTCTTAAATTTAGCTGCAAGAG[T/C]
TAAGTCTGGAGTGGAGTTGTGAAGCTATTTAAACCTAAATCCACCTCTCGTTCATTTTGTGAGAGAGCTCCACCCAGCTCCACACTAATTTTAGATGGAG

Reverse complement sequence

CTCCATCTAAAATTAGTGTGGAGCTGGGTGGAGCTCTCTCACAAAATGAACGAGAGGTGGATTTAGGTTTAAATAGCTTCACAACTCCACTCCAGACTTA[A/G]
CTCTTGCAGCTAAATTTAAGAGTTGGAGCTTTACCAAACAGACCCTATGATTCGTGTAAGTTGTAAGGGAGAAAAATCGCGTGCGGGGGATGACTATAAA

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 95.50% 3.60% 0.85% 0.00% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 87.30% 10.20% 2.51% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.40% 0.25% 0.00% NA
Temperate Japonica  767 81.00% 14.30% 4.69% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 83.00% 16.20% 0.83% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0919588048 T -> C LOC_Os09g32840.1 upstream_gene_variant ; 1838.0bp to feature; MODIFIER silent_mutation Average:88.476; most accessible tissue: Zhenshan97 root, score: 92.977 N N N N
vg0919588048 T -> C LOC_Os09g32850.1 upstream_gene_variant ; 178.0bp to feature; MODIFIER silent_mutation Average:88.476; most accessible tissue: Zhenshan97 root, score: 92.977 N N N N
vg0919588048 T -> C LOC_Os09g32860.1 upstream_gene_variant ; 1494.0bp to feature; MODIFIER silent_mutation Average:88.476; most accessible tissue: Zhenshan97 root, score: 92.977 N N N N
vg0919588048 T -> C LOC_Os09g32860.2 upstream_gene_variant ; 1494.0bp to feature; MODIFIER silent_mutation Average:88.476; most accessible tissue: Zhenshan97 root, score: 92.977 N N N N
vg0919588048 T -> C LOC_Os09g32850-LOC_Os09g32860 intergenic_region ; MODIFIER silent_mutation Average:88.476; most accessible tissue: Zhenshan97 root, score: 92.977 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)
vg0919588048 T C 0.01 -0.02 -0.01 -0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0919588048 NA 1.18E-21 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
vg0919588048 NA 1.64E-08 Awn_length 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
vg0919588048 NA 2.18E-06 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
vg0919588048 NA 2.25E-08 mr1829 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
vg0919588048 2.82E-06 1.83E-12 mr1057_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
vg0919588048 NA 1.47E-06 mr1465_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
vg0919588048 6.71E-07 NA mr1667_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
vg0919588048 4.72E-06 5.07E-06 mr1667_2 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
vg0919588048 NA 1.27E-06 mr1736_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
vg0919588048 NA 4.93E-06 mr1740_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
vg0919588048 NA 4.60E-10 mr1829_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