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Detailed information for vg0125130488:

Variant ID: vg0125130488 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25130488
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


TCACCAAGCTCGAGACGGCGGTGGGCTCATCGCTGCCTTCACGCGAGCTTCGATCGCGACCTCTAGGGCCCTCGCCGTCGAGGTCGTTCCAGCCCCACGC[T/C]
AGCACTCTTTCTGCCCCACTGGCTGAGATCCGGCCTCGACGACCGCACTGGCGCCGTCCACTCTCCCTGGGCAAAGAGTACGGCGATGGAACCCAGGGGA

Reverse complement sequence

TCCCCTGGGTTCCATCGCCGTACTCTTTGCCCAGGGAGAGTGGACGGCGCCAGTGCGGTCGTCGAGGCCGGATCTCAGCCAGTGGGGCAGAAAGAGTGCT[A/G]
GCGTGGGGCTGGAACGACCTCGACGGCGAGGGCCCTAGAGGTCGCGATCGAAGCTCGCGTGAAGGCAGCGATGAGCCCACCGCCGTCTCGAGCTTGGTGA

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 81.40% 18.50% 0.11% 0.00% NA
All Indica  2759 99.60% 0.40% 0.04% 0.00% NA
All Japonica  1512 49.30% 50.40% 0.26% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.50% 0.13% 0.00% NA
Temperate Japonica  767 21.90% 78.00% 0.13% 0.00% NA
Tropical Japonica  504 87.50% 12.50% 0.00% 0.00% NA
Japonica Intermediate  241 56.80% 41.90% 1.24% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0125130488 T -> C LOC_Os01g43870.1 upstream_gene_variant ; 2397.0bp to feature; MODIFIER silent_mutation Average:89.132; most accessible tissue: Minghui63 flag leaf, score: 97.024 N N N N
vg0125130488 T -> C LOC_Os01g43870.3 upstream_gene_variant ; 2397.0bp to feature; MODIFIER silent_mutation Average:89.132; most accessible tissue: Minghui63 flag leaf, score: 97.024 N N N N
vg0125130488 T -> C LOC_Os01g43870.2 upstream_gene_variant ; 2397.0bp to feature; MODIFIER silent_mutation Average:89.132; most accessible tissue: Minghui63 flag leaf, score: 97.024 N N N N
vg0125130488 T -> C LOC_Os01g43870.6 upstream_gene_variant ; 2397.0bp to feature; MODIFIER silent_mutation Average:89.132; most accessible tissue: Minghui63 flag leaf, score: 97.024 N N N N
vg0125130488 T -> C LOC_Os01g43870.4 upstream_gene_variant ; 2399.0bp to feature; MODIFIER silent_mutation Average:89.132; most accessible tissue: Minghui63 flag leaf, score: 97.024 N N N N
vg0125130488 T -> C LOC_Os01g43860.1 downstream_gene_variant ; 521.0bp to feature; MODIFIER silent_mutation Average:89.132; most accessible tissue: Minghui63 flag leaf, score: 97.024 N N N N
vg0125130488 T -> C LOC_Os01g43860-LOC_Os01g43870 intergenic_region ; MODIFIER silent_mutation Average:89.132; most accessible tissue: Minghui63 flag leaf, score: 97.024 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)
vg0125130488 T C 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125130488 NA 6.10E-09 mr1539 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
vg0125130488 NA 1.06E-10 mr1539 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
vg0125130488 NA 4.42E-10 mr1712 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
vg0125130488 NA 1.04E-07 mr1977 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
vg0125130488 NA 5.27E-06 mr1383_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
vg0125130488 NA 2.92E-14 mr1902_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