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Detailed information for vg0205189046:

Variant ID: vg0205189046 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 5189046
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTGAAGTAGTATTTACAAGGGGTGATCATGCATGGATCTCTTCTCCCCGGGTATTTTTTTCCCTTCTAAATCTAGTCTAGTATTGAACAAATTAATTA[A/C]
AGCTTTAAACTTGTGTTAAGCTCTAAGCTTCTGAAAAAAAATACGAAAAAATTGTTTCCCCTAAAAAGAAGGGGGACAAAAAGCTGAATCTTCATCTATC

Reverse complement sequence

GATAGATGAAGATTCAGCTTTTTGTCCCCCTTCTTTTTAGGGGAAACAATTTTTTCGTATTTTTTTTCAGAAGCTTAGAGCTTAACACAAGTTTAAAGCT[T/G]
TAATTAATTTGTTCAATACTAGACTAGATTTAGAAGGGAAAAAAATACCCGGGGAGAAGAGATCCATGCATGATCACCCCTTGTAAATACTACTTCAATC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.30% 4.00% 0.76% 0.00% NA
All Indica  2759 92.50% 6.50% 1.01% 0.00% NA
All Japonica  1512 99.70% 0.20% 0.07% 0.00% NA
Aus  269 98.10% 0.00% 1.86% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 72.30% 23.20% 4.52% 0.00% NA
Indica III  913 96.80% 3.00% 0.22% 0.00% NA
Indica Intermediate  786 93.60% 5.70% 0.64% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 5.60% 2.22% 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
vg0205189046 A -> C LOC_Os02g09980.1 3_prime_UTR_variant ; 102.0bp to feature; MODIFIER silent_mutation Average:83.299; most accessible tissue: Minghui63 flag leaf, score: 96.613 N N N N
vg0205189046 A -> C LOC_Os02g09970.1 upstream_gene_variant ; 4666.0bp to feature; MODIFIER silent_mutation Average:83.299; most accessible tissue: Minghui63 flag leaf, score: 96.613 N N N N
vg0205189046 A -> C LOC_Os02g09990.1 downstream_gene_variant ; 4928.0bp to feature; MODIFIER silent_mutation Average:83.299; most accessible tissue: Minghui63 flag leaf, score: 96.613 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)
vg0205189046 A C 0.05 0.04 0.05 0.03 0.05 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0205189046 NA 2.38E-06 mr1150 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
vg0205189046 NA 6.83E-07 mr1170 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
vg0205189046 NA 7.72E-06 mr1918 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
vg0205189046 NA 1.82E-06 mr1074_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
vg0205189046 1.35E-06 2.64E-06 mr1095_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
vg0205189046 5.49E-06 5.35E-07 mr1098_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
vg0205189046 NA 2.79E-06 mr1148_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
vg0205189046 3.99E-07 4.91E-10 mr1150_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
vg0205189046 NA 3.86E-07 mr1877_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
vg0205189046 5.27E-06 8.94E-08 mr1918_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