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Detailed information for vg0102539858:

Variant ID: vg0102539858 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2539858
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


GACATAGTTTCCATAATCTCCACATCATTAAGAAACTAGCACTAGACACTACTCTTCCAATGCAAACACTACTATTCCATACTTAAATTTAATGATACTT[G/A]
TCTAACATAATGTCTTGGATGTTGTGTAGAAACCATGTCTCATGCAAGACATGGTTTTCTTCTCTTTTTTCATTTATTCACTTGCCACATCATTTTTCAT

Reverse complement sequence

ATGAAAAATGATGTGGCAAGTGAATAAATGAAAAAAGAGAAGAAAACCATGTCTTGCATGAGACATGGTTTCTACACAACATCCAAGACATTATGTTAGA[C/T]
AAGTATCATTAAATTTAAGTATGGAATAGTAGTGTTTGCATTGGAAGAGTAGTGTCTAGTGCTAGTTTCTTAATGATGTGGAGATTATGGAAACTATGTC

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 48.60% 26.30% 0.95% 24.14% NA
All Indica  2759 30.50% 40.40% 1.12% 27.91% NA
All Japonica  1512 81.70% 6.40% 0.53% 11.31% NA
Aus  269 29.70% 1.10% 2.23% 66.91% NA
Indica I  595 10.60% 25.50% 2.35% 61.51% NA
Indica II  465 33.30% 58.50% 0.22% 7.96% NA
Indica III  913 41.30% 37.80% 0.66% 20.26% NA
Indica Intermediate  786 31.40% 44.10% 1.27% 23.16% NA
Temperate Japonica  767 83.20% 12.00% 0.13% 4.69% NA
Tropical Japonica  504 79.60% 0.40% 0.99% 19.05% NA
Japonica Intermediate  241 81.70% 1.20% 0.83% 16.18% NA
VI/Aromatic  96 82.30% 6.20% 0.00% 11.46% NA
Intermediate  90 68.90% 21.10% 0.00% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0102539858 G -> A LOC_Os01g05360.1 downstream_gene_variant ; 4178.0bp to feature; MODIFIER silent_mutation Average:54.939; most accessible tissue: Minghui63 panicle, score: 92.38 N N N N
vg0102539858 G -> A LOC_Os01g05380.1 downstream_gene_variant ; 2155.0bp to feature; MODIFIER silent_mutation Average:54.939; most accessible tissue: Minghui63 panicle, score: 92.38 N N N N
vg0102539858 G -> A LOC_Os01g05370.1 intron_variant ; MODIFIER silent_mutation Average:54.939; most accessible tissue: Minghui63 panicle, score: 92.38 N N N N
vg0102539858 G -> DEL N N silent_mutation Average:54.939; most accessible tissue: Minghui63 panicle, score: 92.38 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)
vg0102539858 G A -0.03 -0.03 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0102539858 NA 2.00E-06 mr1064 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
vg0102539858 2.07E-06 2.07E-06 mr1417 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
vg0102539858 2.37E-06 1.06E-06 mr1544 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