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Detailed information for vg1217580896:

Variant ID: vg1217580896 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 17580896
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.75, T: 0.25, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


CGTGGCCCTCGCTGCCCGGCGTGTGCCCGCCACTAGCCAGCTCTTTCCAGTTTCCCCTGCGCGCCTCGTGATGCTTTGTGTCACTGACAGCGTGGGGCCA[C/T]
GTCCCCGGACGGCTGGGACCGGCCTGTCGGTGATCAGAGGAGAAGACGCTTTTTCTCACCTTCGGATCGGAGAGGAGCCTTTTTTTTTTCTTTTCCAGTT

Reverse complement sequence

AACTGGAAAAGAAAAAAAAAAGGCTCCTCTCCGATCCGAAGGTGAGAAAAAGCGTCTTCTCCTCTGATCACCGACAGGCCGGTCCCAGCCGTCCGGGGAC[G/A]
TGGCCCCACGCTGTCAGTGACACAAAGCATCACGAGGCGCGCAGGGGAAACTGGAAAGAGCTGGCTAGTGGCGGGCACACGCCGGGCAGCGAGGGCCACG

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 49.20% 45.80% 1.10% 3.91% NA
All Indica  2759 46.30% 51.10% 0.36% 2.17% NA
All Japonica  1512 59.90% 31.50% 0.53% 8.07% NA
Aus  269 12.30% 87.40% 0.37% 0.00% NA
Indica I  595 22.00% 78.00% 0.00% 0.00% NA
Indica II  465 51.80% 38.30% 0.86% 9.03% NA
Indica III  913 60.40% 38.70% 0.22% 0.77% NA
Indica Intermediate  786 45.20% 52.90% 0.51% 1.40% NA
Temperate Japonica  767 92.70% 7.20% 0.00% 0.13% NA
Tropical Japonica  504 20.00% 56.70% 1.19% 22.02% NA
Japonica Intermediate  241 38.60% 56.40% 0.83% 4.15% NA
VI/Aromatic  96 60.40% 11.50% 26.04% 2.08% NA
Intermediate  90 54.40% 35.60% 8.89% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1217580896 C -> DEL N N silent_mutation Average:99.863; most accessible tissue: Zhenshan97 panicle, score: 99.957 N N N N
vg1217580896 C -> T LOC_Os12g29520.1 upstream_gene_variant ; 3000.0bp to feature; MODIFIER silent_mutation Average:99.863; most accessible tissue: Zhenshan97 panicle, score: 99.957 N N N N
vg1217580896 C -> T LOC_Os12g29520.2 upstream_gene_variant ; 3000.0bp to feature; MODIFIER silent_mutation Average:99.863; most accessible tissue: Zhenshan97 panicle, score: 99.957 N N N N
vg1217580896 C -> T LOC_Os12g29520.3 upstream_gene_variant ; 3000.0bp to feature; MODIFIER silent_mutation Average:99.863; most accessible tissue: Zhenshan97 panicle, score: 99.957 N N N N
vg1217580896 C -> T LOC_Os12g29520.4 upstream_gene_variant ; 3000.0bp to feature; MODIFIER silent_mutation Average:99.863; most accessible tissue: Zhenshan97 panicle, score: 99.957 N N N N
vg1217580896 C -> T LOC_Os12g29520.5 upstream_gene_variant ; 3000.0bp to feature; MODIFIER silent_mutation Average:99.863; most accessible tissue: Zhenshan97 panicle, score: 99.957 N N N N
vg1217580896 C -> T LOC_Os12g29520-LOC_Os12g29530 intergenic_region ; MODIFIER silent_mutation Average:99.863; most accessible tissue: Zhenshan97 panicle, score: 99.957 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)
vg1217580896 C T -0.03 -0.04 -0.04 -0.03 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1217580896 2.80E-07 2.26E-08 mr1388 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
vg1217580896 NA 3.46E-07 mr1829 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
vg1217580896 NA 8.40E-06 mr1528_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
vg1217580896 NA 1.96E-09 mr1645_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
vg1217580896 NA 7.21E-08 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
vg1217580896 NA 1.34E-06 mr1747_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
vg1217580896 NA 1.07E-06 mr1831_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
vg1217580896 NA 3.15E-07 mr1840_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
vg1217580896 NA 4.68E-08 mr1856_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