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Detailed information for vg0106607583:

Variant ID: vg0106607583 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6607583
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCTACCAGCGAAAATACCATATCTTCGCTGGCGGCTAGCTTAAGACGACCGCCAGCGAAGATAGGTTTTCGCTGGCGGTCCATGACCCCCCACCCTCCCT[T/A]
TTTTTTTATGGCGGTTTTATCTCGTAGCCGCTAGCAAAAATTTTTCCCAAACGCCATGAAAAATTGTTTTTCTAGTAGCATTCGTTGCTCACTATTTTTA

Reverse complement sequence

TAAAAATAGTGAGCAACGAATGCTACTAGAAAAACAATTTTTCATGGCGTTTGGGAAAAATTTTTGCTAGCGGCTACGAGATAAAACCGCCATAAAAAAA[A/T]
AGGGAGGGTGGGGGGTCATGGACCGCCAGCGAAAACCTATCTTCGCTGGCGGTCGTCTTAAGCTAGCCGCCAGCGAAGATATGGTATTTTCGCTGGTAGC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.50% 2.50% 14.75% 16.19% NA
All Indica  2759 61.80% 4.00% 12.98% 21.24% NA
All Japonica  1512 87.40% 0.10% 3.97% 8.60% NA
Aus  269 7.40% 2.20% 76.21% 14.13% NA
Indica I  595 47.70% 0.30% 7.06% 44.87% NA
Indica II  465 71.80% 11.00% 11.83% 5.38% NA
Indica III  913 71.00% 1.40% 8.87% 18.73% NA
Indica Intermediate  786 56.00% 5.50% 22.90% 15.65% NA
Temperate Japonica  767 99.20% 0.00% 0.52% 0.26% NA
Tropical Japonica  504 77.80% 0.20% 9.52% 12.50% NA
Japonica Intermediate  241 69.70% 0.00% 3.32% 26.97% NA
VI/Aromatic  96 34.40% 0.00% 63.54% 2.08% NA
Intermediate  90 72.20% 3.30% 14.44% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0106607583 T -> A LOC_Os01g12120.1 upstream_gene_variant ; 344.0bp to feature; MODIFIER silent_mutation Average:71.285; most accessible tissue: Minghui63 young leaf, score: 96.569 N N N N
vg0106607583 T -> A LOC_Os01g12130.1 downstream_gene_variant ; 4760.0bp to feature; MODIFIER silent_mutation Average:71.285; most accessible tissue: Minghui63 young leaf, score: 96.569 N N N N
vg0106607583 T -> A LOC_Os01g12120-LOC_Os01g12130 intergenic_region ; MODIFIER silent_mutation Average:71.285; most accessible tissue: Minghui63 young leaf, score: 96.569 N N N N
vg0106607583 T -> DEL N N silent_mutation Average:71.285; most accessible tissue: Minghui63 young leaf, score: 96.569 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)
vg0106607583 T A 0.01 0.0 0.0 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106607583 3.68E-10 4.01E-22 mr1498 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
vg0106607583 3.78E-10 6.65E-28 mr1498 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
vg0106607583 NA 1.06E-20 mr1769 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
vg0106607583 1.20E-06 8.62E-23 mr1769 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
vg0106607583 1.86E-06 1.86E-06 mr1916 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
vg0106607583 NA 1.36E-12 mr1925 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
vg0106607583 NA 4.80E-11 mr1925 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
vg0106607583 2.62E-10 8.20E-21 mr1951 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
vg0106607583 2.49E-11 1.18E-21 mr1951 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
vg0106607583 NA 2.48E-10 mr1310_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
vg0106607583 2.11E-07 1.68E-22 mr1498_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
vg0106607583 NA 1.60E-18 mr1498_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
vg0106607583 5.28E-06 1.03E-21 mr1769_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
vg0106607583 5.56E-06 9.45E-25 mr1769_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
vg0106607583 2.48E-08 6.21E-10 mr1916_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
vg0106607583 NA 2.14E-11 mr1925_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
vg0106607583 NA 1.17E-09 mr1925_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
vg0106607583 1.63E-06 8.11E-14 mr1951_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
vg0106607583 4.63E-06 3.12E-14 mr1951_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