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Detailed information for vg0900043410:

Variant ID: vg0900043410 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 43410
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


GAGTAGCTGTTTCCATATTAACGGGAAGGAAGAGAAATTTGAGTTTTAGCCAAGGACTGAACAATGTTCCATGGCCAGAATCAGGAAGATTGCTTGCTCT[G/A]
GCAACAAAATCAACCTAGCAGAGGTCTCTTCTACATCATCTACATCGGCTTGTTTGGCTTCAAATTCTGTAGGCAGCATACAGACCATGTTTACTGATGT

Reverse complement sequence

ACATCAGTAAACATGGTCTGTATGCTGCCTACAGAATTTGAAGCCAAACAAGCCGATGTAGATGATGTAGAAGAGACCTCTGCTAGGTTGATTTTGTTGC[C/T]
AGAGCAAGCAATCTTCCTGATTCTGGCCATGGAACATTGTTCAGTCCTTGGCTAAAACTCAAATTTCTCTTCCTTCCCGTTAATATGGAAACAGCTACTC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.20% 34.00% 2.29% 10.54% NA
All Indica  2759 34.70% 54.00% 2.54% 8.70% NA
All Japonica  1512 85.90% 0.50% 1.19% 12.37% NA
Aus  269 66.90% 32.00% 0.00% 1.12% NA
Indica I  595 42.40% 46.10% 2.18% 9.41% NA
Indica II  465 42.40% 43.90% 3.66% 10.11% NA
Indica III  913 29.00% 61.60% 1.97% 7.45% NA
Indica Intermediate  786 31.00% 57.40% 2.80% 8.78% NA
Temperate Japonica  767 74.80% 0.50% 2.09% 22.56% NA
Tropical Japonica  504 98.00% 0.20% 0.00% 1.79% NA
Japonica Intermediate  241 95.90% 1.20% 0.83% 2.07% NA
VI/Aromatic  96 24.00% 5.20% 15.62% 55.21% NA
Intermediate  90 60.00% 17.80% 5.56% 16.67% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0900043410 G -> DEL N N silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0900043410 G -> A LOC_Os09g01002.1 upstream_gene_variant ; 1752.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0900043410 G -> A LOC_Os09g01006.1 downstream_gene_variant ; 52.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0900043410 G -> A LOC_Os09g01006-LOC_Os09g01010 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 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)
vg0900043410 G A -0.01 0.0 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0900043410 1.46E-06 4.53E-08 mr1168 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
vg0900043410 1.46E-06 5.02E-08 mr1383 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
vg0900043410 NA 1.68E-13 mr1449 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
vg0900043410 6.71E-06 6.70E-06 mr1449 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
vg0900043410 NA 1.12E-06 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
vg0900043410 NA 4.77E-07 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
vg0900043410 4.03E-06 2.61E-09 mr1168_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
vg0900043410 NA 1.66E-07 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