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Detailed information for vg0141059442:

Variant ID: vg0141059442 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 41059442
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:


CGGTGTGATCGGATTATAGATTAGATAAGTAATTTAAGAGAAAATTCGTTTTGAATATCATTAAAGGTGCATGTTATATGGTTGGAGATAGAGATACAGA[C/T]
TTGGATATGTGCATATGTGTTAGAGACTGCCCGTCCGATTTTTCTTGGTGGTTCAAGCATTCGAGAAGAAGCATTTTCTGTCTTGTTTAGGTGATCAACT

Reverse complement sequence

AGTTGATCACCTAAACAAGACAGAAAATGCTTCTTCTCGAATGCTTGAACCACCAAGAAAAATCGGACGGGCAGTCTCTAACACATATGCACATATCCAA[G/A]
TCTGTATCTCTATCTCCAACCATATAACATGCACCTTTAATGATATTCAAAACGAATTTTCTCTTAAATTACTTATCTAATCTATAATCCGATCACACCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 53.70% 46.20% 0.11% 0.00% NA
All Indica  2759 22.90% 76.90% 0.18% 0.00% NA
All Japonica  1512 98.50% 1.50% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 14.80% 85.00% 0.17% 0.00% NA
Indica II  465 3.00% 97.00% 0.00% 0.00% NA
Indica III  913 35.00% 64.70% 0.22% 0.00% NA
Indica Intermediate  786 26.70% 73.00% 0.25% 0.00% NA
Temperate Japonica  767 98.80% 1.20% 0.00% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 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
vg0141059442 C -> T LOC_Os01g70930.1 upstream_gene_variant ; 570.0bp to feature; MODIFIER silent_mutation Average:87.241; most accessible tissue: Minghui63 panicle, score: 95.346 N N N N
vg0141059442 C -> T LOC_Os01g70940.1 upstream_gene_variant ; 1649.0bp to feature; MODIFIER silent_mutation Average:87.241; most accessible tissue: Minghui63 panicle, score: 95.346 N N N N
vg0141059442 C -> T LOC_Os01g70940.2 upstream_gene_variant ; 1649.0bp to feature; MODIFIER silent_mutation Average:87.241; most accessible tissue: Minghui63 panicle, score: 95.346 N N N N
vg0141059442 C -> T LOC_Os01g70940.3 upstream_gene_variant ; 1649.0bp to feature; MODIFIER silent_mutation Average:87.241; most accessible tissue: Minghui63 panicle, score: 95.346 N N N N
vg0141059442 C -> T LOC_Os01g70920.1 downstream_gene_variant ; 2793.0bp to feature; MODIFIER silent_mutation Average:87.241; most accessible tissue: Minghui63 panicle, score: 95.346 N N N N
vg0141059442 C -> T LOC_Os01g70920.2 downstream_gene_variant ; 2793.0bp to feature; MODIFIER silent_mutation Average:87.241; most accessible tissue: Minghui63 panicle, score: 95.346 N N N N
vg0141059442 C -> T LOC_Os01g70920.3 downstream_gene_variant ; 2793.0bp to feature; MODIFIER silent_mutation Average:87.241; most accessible tissue: Minghui63 panicle, score: 95.346 N N N N
vg0141059442 C -> T LOC_Os01g70930-LOC_Os01g70940 intergenic_region ; MODIFIER silent_mutation Average:87.241; most accessible tissue: Minghui63 panicle, score: 95.346 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)
vg0141059442 C T -0.05 -0.06 -0.07 -0.04 -0.05 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0141059442 NA 1.48E-20 mr1244 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
vg0141059442 NA 2.65E-11 mr1457 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
vg0141059442 NA 1.94E-52 mr1458 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
vg0141059442 NA 6.63E-08 mr1458 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
vg0141059442 NA 1.98E-51 mr1063_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
vg0141059442 NA 9.19E-49 mr1111_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
vg0141059442 NA 7.83E-06 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
vg0141059442 NA 1.01E-21 mr1164_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
vg0141059442 NA 1.08E-15 mr1180_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
vg0141059442 NA 1.04E-20 mr1183_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
vg0141059442 NA 9.59E-20 mr1218_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
vg0141059442 NA 1.96E-35 mr1221_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
vg0141059442 NA 3.93E-17 mr1260_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
vg0141059442 NA 5.50E-09 mr1319_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
vg0141059442 NA 1.89E-08 mr1322_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
vg0141059442 NA 5.93E-29 mr1323_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
vg0141059442 NA 2.55E-13 mr1330_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
vg0141059442 NA 2.63E-17 mr1352_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
vg0141059442 NA 3.14E-06 mr1380_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
vg0141059442 NA 2.60E-23 mr1422_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
vg0141059442 NA 4.71E-18 mr1454_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
vg0141059442 NA 8.85E-07 mr1454_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
vg0141059442 NA 8.83E-21 mr1457_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
vg0141059442 NA 2.46E-61 mr1458_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
vg0141059442 NA 1.08E-10 mr1458_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
vg0141059442 NA 1.08E-08 mr1527_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
vg0141059442 NA 2.27E-06 mr1561_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
vg0141059442 NA 1.70E-30 mr1580_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
vg0141059442 NA 9.32E-06 mr1721_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
vg0141059442 NA 1.10E-30 mr1825_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
vg0141059442 5.07E-06 NA mr1875_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
vg0141059442 NA 1.70E-07 mr1875_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
vg0141059442 2.98E-06 NA mr1908_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
vg0141059442 NA 2.88E-07 mr1908_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
vg0141059442 NA 3.02E-06 mr1996_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