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Detailed information for vg0917926619:

Variant ID: vg0917926619 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 17926619
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGTCTTAAATACGACTCTCTAAATTCATTCAGATAAGTAGTTCACCAATCATAGATTGATTTTACGGTCGCACTTGTCTCAAGACTGAGAGACAGAG[C/T]
GTGTCTGCGCCTCTGTGGGGAAGAAGAGAGGTCAGAGGAGGACTACATGTGATCCAATGGTTGGAAAATAACCAATGGGGTTCGGAGTTTTATTTTCCGA

Reverse complement sequence

TCGGAAAATAAAACTCCGAACCCCATTGGTTATTTTCCAACCATTGGATCACATGTAGTCCTCCTCTGACCTCTCTTCTTCCCCACAGAGGCGCAGACAC[G/A]
CTCTGTCTCTCAGTCTTGAGACAAGTGCGACCGTAAAATCAATCTATGATTGGTGAACTACTTATCTGAATGAATTTAGAGAGTCGTATTTAAGACAAAA

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 84.60% 12.80% 2.56% 0.00% NA
All Indica  2759 84.80% 10.80% 4.39% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 20.80% 79.20% 0.00% 0.00% NA
Indica I  595 60.20% 26.20% 13.61% 0.00% NA
Indica II  465 95.70% 3.20% 1.08% 0.00% NA
Indica III  913 96.90% 3.10% 0.00% 0.00% NA
Indica Intermediate  786 83.10% 12.50% 4.45% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 24.00% 76.00% 0.00% 0.00% NA
Intermediate  90 84.40% 15.60% 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
vg0917926619 C -> T LOC_Os09g29480.1 upstream_gene_variant ; 3070.0bp to feature; MODIFIER silent_mutation Average:76.343; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg0917926619 C -> T LOC_Os09g29480.2 upstream_gene_variant ; 3070.0bp to feature; MODIFIER silent_mutation Average:76.343; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg0917926619 C -> T LOC_Os09g29480.3 upstream_gene_variant ; 3070.0bp to feature; MODIFIER silent_mutation Average:76.343; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg0917926619 C -> T LOC_Os09g29470.1 downstream_gene_variant ; 2743.0bp to feature; MODIFIER silent_mutation Average:76.343; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg0917926619 C -> T LOC_Os09g29470.2 downstream_gene_variant ; 3478.0bp to feature; MODIFIER silent_mutation Average:76.343; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg0917926619 C -> T LOC_Os09g29470.3 downstream_gene_variant ; 2743.0bp to feature; MODIFIER silent_mutation Average:76.343; most accessible tissue: Zhenshan97 panicle, score: 90.661 N N N N
vg0917926619 C -> T LOC_Os09g29470-LOC_Os09g29480 intergenic_region ; MODIFIER silent_mutation Average:76.343; most accessible tissue: Zhenshan97 panicle, score: 90.661 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)
vg0917926619 C T -0.01 0.0 -0.01 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0917926619 NA 3.99E-08 mr1138 Ind_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
vg0917926619 NA 1.30E-08 mr1585 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
vg0917926619 3.76E-06 3.61E-10 mr1707 Ind_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
vg0917926619 3.30E-08 6.44E-11 mr1728 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
vg0917926619 7.34E-09 1.22E-15 mr1728 Ind_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
vg0917926619 NA 1.94E-17 mr1765 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
vg0917926619 1.92E-06 6.17E-12 mr1860 Ind_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
vg0917926619 NA 8.76E-08 mr1942 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
vg0917926619 NA 1.12E-07 mr1138_2 Ind_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
vg0917926619 NA 5.62E-08 mr1183_2 Ind_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
vg0917926619 NA 7.89E-07 mr1265_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
vg0917926619 NA 2.66E-06 mr1296_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
vg0917926619 NA 1.58E-06 mr1344_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
vg0917926619 NA 4.85E-06 mr1360_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
vg0917926619 NA 4.03E-06 mr1511_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
vg0917926619 NA 6.20E-07 mr1528_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
vg0917926619 4.25E-06 NA mr1707_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
vg0917926619 5.09E-08 2.63E-10 mr1707_2 Ind_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
vg0917926619 6.95E-06 NA mr1728_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
vg0917926619 5.74E-07 3.60E-15 mr1728_2 Ind_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
vg0917926619 NA 1.71E-09 mr1743_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
vg0917926619 NA 1.15E-06 mr1815_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
vg0917926619 2.24E-06 NA mr1834_2 Ind_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
vg0917926619 NA 1.44E-11 mr1860_2 Ind_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