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Detailed information for vg0916184725:

Variant ID: vg0916184725 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16184725
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTAGTTCCAAAATTTTTCTTTAAACTTTTAACTTTTTCATCACATCAAAATTTTCCTATATATACAAACTTCTAACTTTTCAGTCACATCGTTCCAATTT[C/T]
AACCAAACTTTTAATTTTGGTGTGAACTAAACACACCCTACCTTCATCTCAAAATGTACAAGACTTTGACTATGTACTCAAAGAAGTATAATATCTGGGT

Reverse complement sequence

ACCCAGATATTATACTTCTTTGAGTACATAGTCAAAGTCTTGTACATTTTGAGATGAAGGTAGGGTGTGTTTAGTTCACACCAAAATTAAAAGTTTGGTT[G/A]
AAATTGGAACGATGTGACTGAAAAGTTAGAAGTTTGTATATATAGGAAAATTTTGATGTGATGAAAAAGTTAAAAGTTTAAAGAAAAATTTTGGAACTAA

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 93.60% 5.90% 0.32% 0.21% NA
All Indica  2759 89.60% 9.50% 0.54% 0.36% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 94.80% 5.20% 0.00% 0.00% NA
Indica I  595 68.90% 28.70% 1.01% 1.34% NA
Indica II  465 96.10% 3.90% 0.00% 0.00% NA
Indica III  913 98.90% 1.10% 0.00% 0.00% NA
Indica Intermediate  786 90.70% 7.90% 1.15% 0.25% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0916184725 C -> DEL N N silent_mutation Average:84.774; most accessible tissue: Minghui63 root, score: 93.674 N N N N
vg0916184725 C -> T LOC_Os09g26660.1 upstream_gene_variant ; 1555.0bp to feature; MODIFIER silent_mutation Average:84.774; most accessible tissue: Minghui63 root, score: 93.674 N N N N
vg0916184725 C -> T LOC_Os09g26650-LOC_Os09g26660 intergenic_region ; MODIFIER silent_mutation Average:84.774; most accessible tissue: Minghui63 root, score: 93.674 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)
vg0916184725 C T 0.0 0.02 0.02 -0.01 -0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0916184725 3.92E-06 3.92E-06 mr1370 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
vg0916184725 NA 1.39E-14 mr1707 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
vg0916184725 NA 2.27E-09 mr1707 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
vg0916184725 4.98E-07 4.68E-20 mr1728 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
vg0916184725 NA 2.87E-12 mr1728 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
vg0916184725 NA 6.69E-13 mr1860 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
vg0916184725 NA 7.77E-10 mr1860 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
vg0916184725 NA 4.47E-12 mr1707_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
vg0916184725 NA 5.04E-08 mr1707_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
vg0916184725 NA 3.22E-17 mr1728_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
vg0916184725 NA 2.84E-10 mr1728_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
vg0916184725 NA 7.10E-11 mr1860_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
vg0916184725 NA 3.16E-09 mr1860_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
vg0916184725 NA 1.14E-07 mr1895_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
vg0916184725 NA 3.63E-07 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