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Detailed information for vg1213663935:

Variant ID: vg1213663935 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13663935
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTGAGAGAGAGAGAGATGAGGAAGAGAGAAGAGGGGAAAGAGGGAGAAGAGGCTGACGTGAACATCTGACATGTGGGACCCACATGGATCCCACGCTGA[C/T]
TCAGCCGCCACGTAGACCAAAACCAGGGTCAAAACCACCAAAGGATCTTAGGTGACCAGTTTGCATAGTTAAGGGATCCCACATATCTAGTTTTGCGGTT

Reverse complement sequence

AACCGCAAAACTAGATATGTGGGATCCCTTAACTATGCAAACTGGTCACCTAAGATCCTTTGGTGGTTTTGACCCTGGTTTTGGTCTACGTGGCGGCTGA[G/A]
TCAGCGTGGGATCCATGTGGGTCCCACATGTCAGATGTTCACGTCAGCCTCTTCTCCCTCTTTCCCCTCTTCTCTCTTCCTCATCTCTCTCTCTCTCACT

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 98.80% 0.60% 0.66% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 96.40% 1.70% 1.98% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.30% 0.13% 0.00% NA
Temperate Japonica  767 93.40% 3.30% 3.39% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 0.00% 1.66% 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
vg1213663935 C -> T LOC_Os12g24030.1 upstream_gene_variant ; 2989.0bp to feature; MODIFIER silent_mutation Average:98.349; most accessible tissue: Zhenshan97 panicle, score: 99.669 N N N N
vg1213663935 C -> T LOC_Os12g24050.1 downstream_gene_variant ; 2332.0bp to feature; MODIFIER silent_mutation Average:98.349; most accessible tissue: Zhenshan97 panicle, score: 99.669 N N N N
vg1213663935 C -> T LOC_Os12g24040.1 intron_variant ; MODIFIER silent_mutation Average:98.349; most accessible tissue: Zhenshan97 panicle, score: 99.669 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)
vg1213663935 C T -0.02 0.0 0.04 0.01 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213663935 5.64E-06 5.64E-06 mr1915 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
vg1213663935 3.46E-06 3.46E-06 mr1074_2 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
vg1213663935 2.35E-06 2.35E-06 mr1081_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
vg1213663935 NA 5.14E-06 mr1148_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
vg1213663935 6.51E-06 6.51E-06 mr1342_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
vg1213663935 NA 4.47E-06 mr1405_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
vg1213663935 NA 8.04E-06 mr1482_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
vg1213663935 9.72E-06 9.72E-06 mr1592_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
vg1213663935 NA 1.44E-06 mr1735_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