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Detailed information for vg0904379272:

Variant ID: vg0904379272 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 4379272
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


GGCGGAGGCGATCGTGCGGTGGGGCGCGTGTGAGTGGCTTGCGACCTAAGCGCAGCAGGGGTGCGCACACAAGGAGTAGCAACGTGACTGCAGGATGCAG[T/C]
AGTGGTGAACTCGTCCAACACGATGCAGCGGTGAGCACGCTCGTGGTGAGGATGGCGACCTTGCGGTGGGGTGGTGCATAGTGAGGATGACACGGTAGAG

Reverse complement sequence

CTCTACCGTGTCATCCTCACTATGCACCACCCCACCGCAAGGTCGCCATCCTCACCACGAGCGTGCTCACCGCTGCATCGTGTTGGACGAGTTCACCACT[A/G]
CTGCATCCTGCAGTCACGTTGCTACTCCTTGTGTGCGCACCCCTGCTGCGCTTAGGTCGCAAGCCACTCACACGCGCCCCACCGCACGATCGCCTCCGCC

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 77.50% 22.40% 0.02% 0.00% NA
All Indica  2759 98.00% 2.00% 0.00% 0.00% NA
All Japonica  1512 37.20% 62.70% 0.07% 0.00% NA
Aus  269 85.10% 14.90% 0.00% 0.00% NA
Indica I  595 95.10% 4.90% 0.00% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 97.70% 2.30% 0.00% 0.00% NA
Temperate Japonica  767 2.50% 97.40% 0.13% 0.00% NA
Tropical Japonica  504 84.30% 15.70% 0.00% 0.00% NA
Japonica Intermediate  241 49.40% 50.60% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0904379272 T -> C LOC_Os09g08410.1 upstream_gene_variant ; 101.0bp to feature; MODIFIER silent_mutation Average:86.433; most accessible tissue: Zhenshan97 panicle, score: 95.903 N N N N
vg0904379272 T -> C LOC_Os09g08420.1 downstream_gene_variant ; 3720.0bp to feature; MODIFIER silent_mutation Average:86.433; most accessible tissue: Zhenshan97 panicle, score: 95.903 N N N N
vg0904379272 T -> C LOC_Os09g08410-LOC_Os09g08420 intergenic_region ; MODIFIER silent_mutation Average:86.433; most accessible tissue: Zhenshan97 panicle, score: 95.903 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)
vg0904379272 T C 0.05 0.0 0.01 0.05 0.04 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0904379272 NA 6.00E-09 mr1533 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
vg0904379272 NA 1.22E-06 mr1606 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
vg0904379272 NA 8.25E-06 mr1657 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
vg0904379272 NA 8.43E-10 mr1916 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
vg0904379272 NA 2.11E-24 mr1115_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
vg0904379272 NA 9.10E-18 mr1156_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
vg0904379272 NA 1.47E-06 mr1277_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
vg0904379272 NA 4.23E-08 mr1578_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