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Detailed information for vg1102442316:

Variant ID: vg1102442316 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2442316
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, C: 0.03, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


TGTTGATGCCTTGGGACAGTAAGAGATCTGTTGCAAAGATCAGCAAAGAGCATTTCGAGTTGGAACTAAAACTCAACAGTGTGTTAAATGTTCTGCTTTC[T/C]
GTTTTGCCGTCAAGCTAGCTGCTACAGTACTACCCATAGGCTATAAAAGCAGATACAATAGCAGGCTATAAGCCAGCTATAAATATATTTTAAAAAGATA

Reverse complement sequence

TATCTTTTTAAAATATATTTATAGCTGGCTTATAGCCTGCTATTGTATCTGCTTTTATAGCCTATGGGTAGTACTGTAGCAGCTAGCTTGACGGCAAAAC[A/G]
GAAAGCAGAACATTTAACACACTGTTGAGTTTTAGTTCCAACTCGAAATGCTCTTTGCTGATCTTTGCAACAGATCTCTTACTGTCCCAAGGCATCAACA

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 62.30% 37.30% 0.21% 0.17% NA
All Indica  2759 38.50% 60.90% 0.36% 0.29% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 76.60% 23.40% 0.00% 0.00% NA
Indica I  595 4.90% 94.60% 0.50% 0.00% NA
Indica II  465 61.30% 37.40% 0.43% 0.86% NA
Indica III  913 42.70% 56.80% 0.22% 0.22% NA
Indica Intermediate  786 45.40% 53.90% 0.38% 0.25% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg1102442316 T -> DEL N N silent_mutation Average:68.16; most accessible tissue: Callus, score: 91.291 N N N N
vg1102442316 T -> C LOC_Os11g05430.1 upstream_gene_variant ; 346.0bp to feature; MODIFIER silent_mutation Average:68.16; most accessible tissue: Callus, score: 91.291 N N N N
vg1102442316 T -> C LOC_Os11g05420.1 downstream_gene_variant ; 2323.0bp to feature; MODIFIER silent_mutation Average:68.16; most accessible tissue: Callus, score: 91.291 N N N N
vg1102442316 T -> C LOC_Os11g05440.1 downstream_gene_variant ; 2909.0bp to feature; MODIFIER silent_mutation Average:68.16; most accessible tissue: Callus, score: 91.291 N N N N
vg1102442316 T -> C LOC_Os11g05420-LOC_Os11g05430 intergenic_region ; MODIFIER silent_mutation Average:68.16; most accessible tissue: Callus, score: 91.291 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)
vg1102442316 T C 0.0 0.01 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102442316 NA 2.48E-09 mr1050 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
vg1102442316 NA 4.01E-12 mr1272 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
vg1102442316 NA 2.01E-07 mr1272 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
vg1102442316 NA 1.19E-09 mr1439 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
vg1102442316 8.51E-07 5.24E-25 mr1598 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
vg1102442316 NA 6.23E-10 mr1598 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
vg1102442316 NA 1.34E-07 mr1680 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
vg1102442316 NA 2.24E-11 mr1904 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
vg1102442316 NA 4.23E-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
vg1102442316 NA 3.15E-09 mr1050_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
vg1102442316 NA 6.76E-08 mr1174_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
vg1102442316 NA 2.40E-09 mr1299_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
vg1102442316 NA 7.49E-06 mr1299_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
vg1102442316 NA 7.46E-06 mr1360_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
vg1102442316 NA 9.54E-06 mr1497_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
vg1102442316 NA 1.11E-07 mr1557_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
vg1102442316 NA 1.36E-35 mr1598_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
vg1102442316 NA 6.33E-11 mr1598_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
vg1102442316 NA 7.27E-07 mr1655_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
vg1102442316 NA 8.13E-09 mr1700_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
vg1102442316 NA 2.35E-07 mr1727_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
vg1102442316 NA 1.26E-12 mr1756_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
vg1102442316 3.12E-06 9.12E-09 mr1756_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
vg1102442316 NA 8.63E-09 mr1861_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
vg1102442316 NA 5.85E-06 mr1895_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
vg1102442316 NA 9.31E-14 mr1904_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