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Detailed information for vg1125763864:

Variant ID: vg1125763864 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25763864
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.63, T: 0.37, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTCTATCTCAGATTTTGAACTAAATTTGAAGTTGAACCAAAAAAAAAAAAAGGAGAAATTACGCTCAGATTCGAGGGGGAAGAGCCTAACCAAGGAAA[C/T]
CAGCCACGCGCACCACCGACGAGGACGCCTTGCCGCCGCCGCCGCCGCGGCAGATGGGGAGGCGCTGCGCCGCCGGAAAGGGTCGCCGGCGAGCCGCCCA

Reverse complement sequence

TGGGCGGCTCGCCGGCGACCCTTTCCGGCGGCGCAGCGCCTCCCCATCTGCCGCGGCGGCGGCGGCGGCAAGGCGTCCTCGTCGGTGGTGCGCGTGGCTG[G/A]
TTTCCTTGGTTAGGCTCTTCCCCCTCGAATCTGAGCGTAATTTCTCCTTTTTTTTTTTTTGGTTCAACTTCAAATTTAGTTCAAAATCTGAGATAGAAAC

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 58.70% 41.10% 0.15% 0.00% NA
All Indica  2759 64.40% 35.40% 0.22% 0.00% NA
All Japonica  1512 48.90% 51.00% 0.07% 0.00% NA
Aus  269 56.10% 43.90% 0.00% 0.00% NA
Indica I  595 22.00% 78.00% 0.00% 0.00% NA
Indica II  465 76.10% 23.40% 0.43% 0.00% NA
Indica III  913 74.00% 25.60% 0.33% 0.00% NA
Indica Intermediate  786 78.20% 21.60% 0.13% 0.00% NA
Temperate Japonica  767 25.00% 75.00% 0.00% 0.00% NA
Tropical Japonica  504 81.70% 18.10% 0.20% 0.00% NA
Japonica Intermediate  241 56.40% 43.60% 0.00% 0.00% NA
VI/Aromatic  96 57.30% 42.70% 0.00% 0.00% NA
Intermediate  90 60.00% 40.00% 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
vg1125763864 C -> T LOC_Os11g42780.1 upstream_gene_variant ; 1129.0bp to feature; MODIFIER silent_mutation Average:84.227; most accessible tissue: Zhenshan97 flag leaf, score: 97.707 N N N N
vg1125763864 C -> T LOC_Os11g42770.1 downstream_gene_variant ; 649.0bp to feature; MODIFIER silent_mutation Average:84.227; most accessible tissue: Zhenshan97 flag leaf, score: 97.707 N N N N
vg1125763864 C -> T LOC_Os11g42790.1 downstream_gene_variant ; 4601.0bp to feature; MODIFIER silent_mutation Average:84.227; most accessible tissue: Zhenshan97 flag leaf, score: 97.707 N N N N
vg1125763864 C -> T LOC_Os11g42770-LOC_Os11g42780 intergenic_region ; MODIFIER silent_mutation Average:84.227; most accessible tissue: Zhenshan97 flag leaf, score: 97.707 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)
vg1125763864 C T -0.04 -0.05 -0.05 -0.04 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125763864 NA 2.67E-06 mr1046 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
vg1125763864 6.59E-06 5.19E-07 mr1048 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
vg1125763864 NA 6.72E-06 mr1063 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
vg1125763864 NA 1.46E-07 mr1206 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
vg1125763864 NA 5.47E-06 mr1283 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
vg1125763864 4.85E-06 5.58E-07 mr1288 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
vg1125763864 NA 1.97E-06 mr1378 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
vg1125763864 NA 1.56E-06 mr1496 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
vg1125763864 NA 2.62E-08 mr1549 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
vg1125763864 NA 5.80E-07 mr1570 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
vg1125763864 NA 6.48E-08 mr1662 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
vg1125763864 NA 4.94E-06 mr1676 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
vg1125763864 NA 3.20E-09 mr1745 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
vg1125763864 NA 4.50E-11 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
vg1125763864 NA 6.28E-07 mr1880 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
vg1125763864 NA 7.20E-06 mr1904 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
vg1125763864 NA 1.98E-07 mr1133_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
vg1125763864 NA 3.31E-07 mr1530_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
vg1125763864 NA 2.86E-06 mr1662_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
vg1125763864 NA 2.39E-09 mr1745_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