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Detailed information for vg0901023936:

Variant ID: vg0901023936 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 1023936
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACAATTGTTGACATACAGATCCACGTCTTATAAAAATAGAAAAGATTACAAATGCAGCGGAAAAGATAAAAGCGAGCTAAACTTGGAAGCTTGACTTCTG[C/T]
AGCGGGGCGACTCCACTCCACAGGCAATCCTTGATGGCAGCGACGAAACCAACTTCGACAAGACAGCTCCAACTAGGAAGATCTTCAGCTCTGGTGTGGG

Reverse complement sequence

CCCACACCAGAGCTGAAGATCTTCCTAGTTGGAGCTGTCTTGTCGAAGTTGGTTTCGTCGCTGCCATCAAGGATTGCCTGTGGAGTGGAGTCGCCCCGCT[G/A]
CAGAAGTCAAGCTTCCAAGTTTAGCTCGCTTTTATCTTTTCCGCTGCATTTGTAATCTTTTCTATTTTTATAAGACGTGGATCTGTATGTCAACAATTGT

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 61.20% 9.00% 6.28% 23.53% NA
All Indica  2759 50.20% 0.60% 10.29% 38.85% NA
All Japonica  1512 73.90% 25.40% 0.20% 0.53% NA
Aus  269 92.60% 0.00% 0.74% 6.69% NA
Indica I  595 30.80% 1.20% 12.61% 55.46% NA
Indica II  465 52.30% 0.20% 10.32% 37.20% NA
Indica III  913 59.40% 0.30% 11.06% 29.24% NA
Indica Intermediate  786 53.20% 0.80% 7.63% 38.42% NA
Temperate Japonica  767 97.50% 2.00% 0.39% 0.13% NA
Tropical Japonica  504 36.30% 62.70% 0.00% 0.99% NA
Japonica Intermediate  241 77.20% 22.00% 0.00% 0.83% NA
VI/Aromatic  96 93.80% 5.20% 0.00% 1.04% NA
Intermediate  90 57.80% 18.90% 8.89% 14.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0901023936 C -> DEL N N silent_mutation Average:40.431; most accessible tissue: Zhenshan97 flag leaf, score: 85.259 N N N N
vg0901023936 C -> T LOC_Os09g02460.1 upstream_gene_variant ; 979.0bp to feature; MODIFIER silent_mutation Average:40.431; most accessible tissue: Zhenshan97 flag leaf, score: 85.259 N N N N
vg0901023936 C -> T LOC_Os09g02470.1 upstream_gene_variant ; 3039.0bp to feature; MODIFIER silent_mutation Average:40.431; most accessible tissue: Zhenshan97 flag leaf, score: 85.259 N N N N
vg0901023936 C -> T LOC_Os09g02460-LOC_Os09g02470 intergenic_region ; MODIFIER silent_mutation Average:40.431; most accessible tissue: Zhenshan97 flag leaf, score: 85.259 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)
vg0901023936 C T -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0901023936 NA 7.22E-12 Grain_width Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901023936 NA 4.51E-06 mr1104 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
vg0901023936 4.27E-06 2.46E-07 mr1155 Jap_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
vg0901023936 NA 1.96E-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
vg0901023936 NA 1.60E-07 mr1206 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
vg0901023936 4.25E-06 4.25E-06 mr1208 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
vg0901023936 NA 9.22E-06 mr1213 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
vg0901023936 NA 6.51E-07 mr1229 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
vg0901023936 NA 5.28E-09 mr1229 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
vg0901023936 NA 3.65E-08 mr1554 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
vg0901023936 NA 4.34E-06 mr1596 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
vg0901023936 4.07E-06 NA mr1949 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
vg0901023936 1.48E-07 NA mr1104_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
vg0901023936 5.58E-06 NA mr1107_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
vg0901023936 NA 2.91E-06 mr1206_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
vg0901023936 1.32E-06 NA mr1226_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
vg0901023936 NA 9.01E-06 mr1425_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
vg0901023936 NA 5.60E-06 mr1786_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