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Detailed information for vg0314061468:

Variant ID: vg0314061468 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 14061468
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCGTCCGTGTGGGGCGACTTCTTCATCACCTACGCCCCTTCCAACTCACAGGCATGCAGATTAAACAGTACTGTGCATATATATATATACTTAGGTCTT[A/G]
TTTAAGGAGCTTCTAGCATCTGCAGTTTGTATCATAATCTTCAACTCTCTTAAATATTCTCGTCCTACTTTATAGAATCCAGAAAATAAGGTACAAACCA

Reverse complement sequence

TGGTTTGTACCTTATTTTCTGGATTCTATAAAGTAGGACGAGAATATTTAAGAGAGTTGAAGATTATGATACAAACTGCAGATGCTAGAAGCTCCTTAAA[T/C]
AAGACCTAAGTATATATATATATGCACAGTACTGTTTAATCTGCATGCCTGTGAGTTGGAAGGGGCGTAGGTGATGAAGAAGTCGCCCCACACGGACGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.70% 4.70% 1.93% 0.66% NA
All Indica  2759 99.40% 0.00% 0.00% 0.58% NA
All Japonica  1512 79.00% 14.50% 5.75% 0.73% NA
Aus  269 98.50% 0.00% 0.00% 1.49% NA
Indica I  595 98.30% 0.00% 0.00% 1.68% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.00% 0.00% 0.22% NA
Indica Intermediate  786 99.50% 0.00% 0.00% 0.51% NA
Temperate Japonica  767 64.90% 27.10% 7.95% 0.00% NA
Tropical Japonica  504 96.00% 0.40% 1.39% 2.18% NA
Japonica Intermediate  241 88.40% 3.70% 7.88% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 3.30% 4.44% 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
vg0314061468 A -> DEL N N silent_mutation Average:70.281; most accessible tissue: Minghui63 panicle, score: 91.586 N N N N
vg0314061468 A -> G LOC_Os03g24680.1 intron_variant ; MODIFIER silent_mutation Average:70.281; most accessible tissue: Minghui63 panicle, score: 91.586 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)
vg0314061468 A G 0.01 0.0 0.0 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0314061468 7.08E-07 7.07E-07 mr1609 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