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Detailed information for vg0424007589:

Variant ID: vg0424007589 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24007589
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCGGCGGACTCGCGGAGGAAGAAGCGCGCGACGCTACACATGGACATATCCACTGTGGCGAACATCTCCGCCAGCAACGGCAAGCACAACGCGTCCGCC[G/C]
CCCACACCACCGCCCCCACTGCCGTCGCCATGCCCAGGCTGACCATGCTCCACCGCCTTGCCCCGACGCATATGCACGGACGTCTCGAAATCCTCCTCCT

Reverse complement sequence

AGGAGGAGGATTTCGAGACGTCCGTGCATATGCGTCGGGGCAAGGCGGTGGAGCATGGTCAGCCTGGGCATGGCGACGGCAGTGGGGGCGGTGGTGTGGG[C/G]
GGCGGACGCGTTGTGCTTGCCGTTGCTGGCGGAGATGTTCGCCACAGTGGATATGTCCATGTGTAGCGTCGCGCGCTTCTTCCTCCGCGAGTCCGCCGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.90% 4.00% 0.02% 0.00% NA
All Indica  2759 94.50% 5.50% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 87.40% 12.60% 0.00% 0.00% NA
Indica I  595 93.40% 6.60% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 91.00% 9.00% 0.00% 0.00% NA
Indica Intermediate  786 96.10% 3.80% 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 96.90% 3.10% 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
vg0424007589 G -> C LOC_Os04g40390.1 missense_variant ; p.Ala95Pro; MODERATE nonsynonymous_codon ; A95P Average:93.891; most accessible tissue: Zhenshan97 flag leaf, score: 98.629 unknown unknown DELETERIOUS 0.00

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)
vg0424007589 G C 0.02 0.01 0.02 0.02 0.03 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424007589 NA 9.24E-08 mr1676_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
vg0424007589 1.79E-07 3.11E-09 mr1708_2 Ind_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