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Detailed information for vg0336113969:

Variant ID: vg0336113969 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 36113969
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATTATAATTTTGCAAAATTTGAGATATGCCATCCTGACCCACATGTCATTTACTCATGTGGGTCCTACATGTCATTGAGATACTGATGGCATATGTCAAA[C/T]
TTTGCAAAATTATAATGGCATGGTTCCAATTTACCTTCTTCTTTTTTTTTAGAAGTTCCAGTGTTGCAGCCAAGTCGGAAGTCGCCATTCGTCTTCTCTC

Reverse complement sequence

GAGAGAAGACGAATGGCGACTTCCGACTTGGCTGCAACACTGGAACTTCTAAAAAAAAAGAAGAAGGTAAATTGGAACCATGCCATTATAATTTTGCAAA[G/A]
TTTGACATATGCCATCAGTATCTCAATGACATGTAGGACCCACATGAGTAAATGACATGTGGGTCAGGATGGCATATCTCAAATTTTGCAAAATTATAAT

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 93.10% 6.90% 0.04% 0.00% NA
All Indica  2759 88.80% 11.10% 0.07% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 93.70% 6.30% 0.00% 0.00% NA
Indica I  595 96.60% 3.40% 0.00% 0.00% NA
Indica II  465 94.80% 5.20% 0.00% 0.00% NA
Indica III  913 78.80% 21.10% 0.11% 0.00% NA
Indica Intermediate  786 91.10% 8.80% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 98.90% 1.10% 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
vg0336113969 C -> T LOC_Os03g63920.1 upstream_gene_variant ; 51.0bp to feature; MODIFIER silent_mutation Average:83.284; most accessible tissue: Zhenshan97 panicle, score: 88.625 N N N N
vg0336113969 C -> T LOC_Os03g63910.1 downstream_gene_variant ; 3027.0bp to feature; MODIFIER silent_mutation Average:83.284; most accessible tissue: Zhenshan97 panicle, score: 88.625 N N N N
vg0336113969 C -> T LOC_Os03g63910-LOC_Os03g63920 intergenic_region ; MODIFIER silent_mutation Average:83.284; most accessible tissue: Zhenshan97 panicle, score: 88.625 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)
vg0336113969 C T 0.01 0.04 0.07 0.02 0.05 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0336113969 5.93E-06 7.20E-08 mr1291 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
vg0336113969 4.41E-06 2.75E-07 mr1291 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
vg0336113969 8.88E-06 NA mr1471 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
vg0336113969 NA 9.21E-06 mr1471 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
vg0336113969 NA 3.30E-06 mr1553 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
vg0336113969 9.28E-08 2.24E-09 mr1892 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
vg0336113969 1.87E-07 4.06E-08 mr1892 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