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Detailed information for vg1001208884:

Variant ID: vg1001208884 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 1208884
Reference Allele: CAlternative Allele: A,T
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CACATGGGATGGGATGGTGACAGGGATGTGATGTGAATAGCTTGCACATCTCAAATGCTCAAACAACTTTTATGATGGGTGTGCTGCCATTGTATAGTTA[C/A,T]
TTCCTACTTCTATCCACAGATATAAGCATTCCAAGCATTTACATTTTGTCTGTAAATAAAACCATATTAGAGTACTACGTCTCTTATCCATCATCTCTTA

Reverse complement sequence

TAAGAGATGATGGATAAGAGACGTAGTACTCTAATATGGTTTTATTTACAGACAAAATGTAAATGCTTGGAATGCTTATATCTGTGGATAGAAGTAGGAA[G/T,A]
TAACTATACAATGGCAGCACACCCATCATAAAAGTTGTTTGAGCATTTGAGATGTGCAAGCTATTCACATCACATCCCTGTCACCATCCCATCCCATGTG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.60% 5.50% 0.17% 3.68% T: 0.04%
All Indica  2759 84.30% 9.20% 0.25% 6.09% T: 0.07%
All Japonica  1512 99.80% 0.10% 0.00% 0.07% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.70% 1.30% 0.00% 0.00% NA
Indica II  465 67.10% 29.20% 0.43% 3.23% NA
Indica III  913 82.90% 5.00% 0.55% 11.50% NA
Indica Intermediate  786 85.40% 8.30% 0.00% 6.11% T: 0.25%
Temperate Japonica  767 99.70% 0.10% 0.00% 0.13% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 87.80% 5.60% 1.11% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1001208884 C -> T LOC_Os10g02930-LOC_Os10g02940 intergenic_region ; MODIFIER silent_mutation Average:87.563; most accessible tissue: Zhenshan97 flower, score: 98.45 N N N N
vg1001208884 C -> A LOC_Os10g02930-LOC_Os10g02940 intergenic_region ; MODIFIER silent_mutation Average:87.563; most accessible tissue: Zhenshan97 flower, score: 98.45 N N N N
vg1001208884 C -> DEL N N silent_mutation Average:87.563; most accessible tissue: Zhenshan97 flower, score: 98.45 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)
vg1001208884 C A 0.12 -0.07 -0.08 -0.08 -0.14 -0.16
vg1001208884 C T 0.03 -0.03 -0.03 -0.07 -0.08 -0.1

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1001208884 1.39E-15 NA mr1486 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
vg1001208884 1.14E-17 1.79E-15 mr1486 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
vg1001208884 2.12E-14 NA mr1548 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
vg1001208884 3.28E-14 1.39E-11 mr1548 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
vg1001208884 1.01E-09 NA mr1588 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
vg1001208884 5.27E-11 2.75E-12 mr1588 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
vg1001208884 NA 1.65E-07 mr1158_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
vg1001208884 NA 6.89E-08 mr1158_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
vg1001208884 5.36E-17 NA mr1486_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
vg1001208884 1.20E-19 1.87E-21 mr1486_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
vg1001208884 7.98E-16 NA mr1588_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
vg1001208884 8.53E-17 1.69E-19 mr1588_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