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Detailed information for vg0107047840:

Variant ID: vg0107047840 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 7047840
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:


TACAATTTTTCTTTTGATTACATGGCAAACGTGAGCACACACGTAACATCTCACTCACACATGTGAATGCGTCCCCTAACACATGCTCAAACCAACGGTA[T/C]
ATTATTGATTTCATTAAAGTCCTGTTGAAAACCTACGCGTCCCCTAACACATGCTCTAAAAACAGAAACCAACGACATACTACTGAAATTATTAAAGTCT

Reverse complement sequence

AGACTTTAATAATTTCAGTAGTATGTCGTTGGTTTCTGTTTTTAGAGCATGTGTTAGGGGACGCGTAGGTTTTCAACAGGACTTTAATGAAATCAATAAT[A/G]
TACCGTTGGTTTGAGCATGTGTTAGGGGACGCATTCACATGTGTGAGTGAGATGTTACGTGTGTGCTCACGTTTGCCATGTAATCAAAAGAAAAATTGTA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.90% 45.60% 0.11% 0.47% NA
All Indica  2759 45.80% 53.40% 0.07% 0.80% NA
All Japonica  1512 77.70% 22.20% 0.07% 0.00% NA
Aus  269 2.60% 97.40% 0.00% 0.00% NA
Indica I  595 14.30% 85.40% 0.00% 0.34% NA
Indica II  465 60.20% 39.60% 0.00% 0.22% NA
Indica III  913 46.20% 52.70% 0.11% 0.99% NA
Indica Intermediate  786 60.60% 38.00% 0.13% 1.27% NA
Temperate Japonica  767 97.80% 2.20% 0.00% 0.00% NA
Tropical Japonica  504 41.90% 58.10% 0.00% 0.00% NA
Japonica Intermediate  241 88.80% 10.80% 0.41% 0.00% NA
VI/Aromatic  96 43.80% 54.20% 2.08% 0.00% NA
Intermediate  90 65.60% 34.40% 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
vg0107047840 T -> DEL N N silent_mutation Average:90.881; most accessible tissue: Minghui63 flag leaf, score: 99.262 N N N N
vg0107047840 T -> C LOC_Os01g12740.1 upstream_gene_variant ; 433.0bp to feature; MODIFIER silent_mutation Average:90.881; most accessible tissue: Minghui63 flag leaf, score: 99.262 N N N N
vg0107047840 T -> C LOC_Os01g12720.1 downstream_gene_variant ; 4915.0bp to feature; MODIFIER silent_mutation Average:90.881; most accessible tissue: Minghui63 flag leaf, score: 99.262 N N N N
vg0107047840 T -> C LOC_Os01g12730.1 downstream_gene_variant ; 281.0bp to feature; MODIFIER silent_mutation Average:90.881; most accessible tissue: Minghui63 flag leaf, score: 99.262 N N N N
vg0107047840 T -> C LOC_Os01g12730.2 downstream_gene_variant ; 281.0bp to feature; MODIFIER silent_mutation Average:90.881; most accessible tissue: Minghui63 flag leaf, score: 99.262 N N N N
vg0107047840 T -> C LOC_Os01g12730-LOC_Os01g12740 intergenic_region ; MODIFIER silent_mutation Average:90.881; most accessible tissue: Minghui63 flag leaf, score: 99.262 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)
vg0107047840 T C -0.12 0.01 0.07 0.03 0.05 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0107047840 NA 1.78E-06 mr1236 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
vg0107047840 NA 1.76E-06 mr1364 Jap_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
vg0107047840 1.74E-10 NA 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
vg0107047840 7.57E-08 NA 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
vg0107047840 1.82E-07 NA mr1518 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
vg0107047840 9.77E-06 7.79E-11 mr1518 Jap_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
vg0107047840 NA 1.33E-08 mr1662 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
vg0107047840 3.06E-09 NA mr1676 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
vg0107047840 7.95E-07 4.93E-12 mr1676 Jap_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
vg0107047840 4.62E-07 4.41E-23 mr1699 Jap_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
vg0107047840 NA 3.76E-07 mr1709 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
vg0107047840 NA 2.52E-07 mr1746 Jap_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
vg0107047840 4.41E-08 2.46E-10 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
vg0107047840 4.83E-06 6.64E-21 mr1769 Jap_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
vg0107047840 NA 1.14E-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
vg0107047840 8.37E-07 NA mr1951 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
vg0107047840 NA 3.42E-10 mr1951 Jap_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
vg0107047840 NA 1.87E-06 mr1993 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
vg0107047840 NA 5.07E-06 mr1236_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
vg0107047840 NA 2.86E-06 mr1236_2 Jap_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
vg0107047840 1.95E-16 5.47E-15 mr1498_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
vg0107047840 3.79E-09 1.42E-08 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
vg0107047840 3.69E-09 7.63E-12 mr1498_2 Jap_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
vg0107047840 3.92E-06 1.45E-12 mr1676_2 Jap_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
vg0107047840 9.71E-10 NA mr1699_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
vg0107047840 3.09E-06 NA mr1699_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
vg0107047840 NA 7.98E-20 mr1699_2 Jap_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
vg0107047840 NA 3.29E-08 mr1746_2 Jap_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
vg0107047840 1.23E-13 5.70E-17 mr1769_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
vg0107047840 6.33E-07 NA 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
vg0107047840 2.56E-09 1.00E-24 mr1769_2 Jap_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
vg0107047840 NA 3.55E-06 mr1795_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
vg0107047840 NA 2.87E-10 mr1916_2 Jap_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
vg0107047840 4.92E-11 7.21E-10 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
vg0107047840 6.53E-08 5.27E-08 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
vg0107047840 1.13E-09 2.22E-06 mr1951_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
vg0107047840 2.15E-07 4.53E-08 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
vg0107047840 NA 9.73E-06 mr1951_2 Jap_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