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Detailed information for vg0134190896:

Variant ID: vg0134190896 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34190896
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 336. )

Flanking Sequence (100 bp) in Reference Genome:


ACGCTTGTAAATGCGCCAGCAGCCAGCTTAATTTGTTGTGTACTAGGAAGCCATCGATGACAAATATCGCCTAGAAACCGCACGCATGTTCGCCTGTCCA[T/A]
CCACCGGTGGCTTCCTTCCTATCGCTGCCCAAGTGTGTAGTGAGTGCCCCGGCAAGGCGATCAGTGGATATGTGGCAAGATAAGGGAAAACAGAACCGTC

Reverse complement sequence

GACGGTTCTGTTTTCCCTTATCTTGCCACATATCCACTGATCGCCTTGCCGGGGCACTCACTACACACTTGGGCAGCGATAGGAAGGAAGCCACCGGTGG[A/T]
TGGACAGGCGAACATGCGTGCGGTTTCTAGGCGATATTTGTCATCGATGGCTTCCTAGTACACAACAAATTAAGCTGGCTGCTGGCGCATTTACAAGCGT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 94.60% 5.40% 0.02% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 83.30% 16.70% 0.07% 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  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 85.90% 14.00% 0.13% 0.00% NA
Tropical Japonica  504 89.50% 10.50% 0.00% 0.00% NA
Japonica Intermediate  241 61.80% 38.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0134190896 T -> A LOC_Os01g59180.1 upstream_gene_variant ; 4031.0bp to feature; MODIFIER silent_mutation Average:92.009; most accessible tissue: Zhenshan97 flower, score: 98.812 N N N N
vg0134190896 T -> A LOC_Os01g59190.1 upstream_gene_variant ; 2084.0bp to feature; MODIFIER silent_mutation Average:92.009; most accessible tissue: Zhenshan97 flower, score: 98.812 N N N N
vg0134190896 T -> A LOC_Os01g59180-LOC_Os01g59190 intergenic_region ; MODIFIER silent_mutation Average:92.009; most accessible tissue: Zhenshan97 flower, score: 98.812 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)
vg0134190896 T A 0.01 -0.05 -0.04 -0.01 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134190896 NA 2.11E-11 mr1693 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
vg0134190896 NA 2.92E-07 mr1693 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
vg0134190896 2.54E-06 NA mr1679_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
vg0134190896 NA 5.51E-10 mr1691_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
vg0134190896 NA 2.73E-06 mr1691_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
vg0134190896 1.04E-07 NA mr1720_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
vg0134190896 NA 1.50E-06 mr1720_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