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Detailed information for vg1215507555:

Variant ID: vg1215507555 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15507555
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAGGGTGGGAGGGGCACGAGCAGAGGGCAGCAGCTGTGACGGTGGAGTGGATGGATCCGGCAGCGGGCAATGAAGGAGACGGGCGGACACGGTGGAGGA[G/C]
ATGGATCTGGTGGCAGCTGCCATGACGACGACGACGGCCAGGCCTCCAGAAGGTTCCGGTGGCTCCTACAACCCCCTCCCCTCTCCCAGATCTAATAGGA

Reverse complement sequence

TCCTATTAGATCTGGGAGAGGGGAGGGGGTTGTAGGAGCCACCGGAACCTTCTGGAGGCCTGGCCGTCGTCGTCGTCATGGCAGCTGCCACCAGATCCAT[C/G]
TCCTCCACCGTGTCCGCCCGTCTCCTTCATTGCCCGCTGCCGGATCCATCCACTCCACCGTCACAGCTGCTGCCCTCTGCTCGTGCCCCTCCCACCCTCA

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 85.60% 0.30% 1.48% 12.65% NA
All Indica  2759 95.30% 0.00% 0.51% 4.24% NA
All Japonica  1512 72.90% 0.80% 2.84% 23.41% NA
Aus  269 69.10% 0.00% 2.23% 28.62% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 83.00% 0.00% 2.15% 14.84% NA
Indica III  913 98.20% 0.00% 0.11% 1.64% NA
Indica Intermediate  786 95.40% 0.00% 0.38% 4.20% NA
Temperate Japonica  767 93.00% 1.60% 3.13% 2.35% NA
Tropical Japonica  504 39.30% 0.00% 3.17% 57.54% NA
Japonica Intermediate  241 79.70% 0.00% 1.24% 19.09% NA
VI/Aromatic  96 54.20% 0.00% 4.17% 41.67% NA
Intermediate  90 85.60% 0.00% 3.33% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1215507555 G -> C LOC_Os12g26540.1 upstream_gene_variant ; 2110.0bp to feature; MODIFIER silent_mutation Average:47.07; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg1215507555 G -> C LOC_Os12g26520.1 downstream_gene_variant ; 2880.0bp to feature; MODIFIER silent_mutation Average:47.07; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg1215507555 G -> C LOC_Os12g26530.1 intron_variant ; MODIFIER silent_mutation Average:47.07; most accessible tissue: Zhenshan97 panicle, score: 92.66 N N N N
vg1215507555 G -> DEL N N silent_mutation Average:47.07; most accessible tissue: Zhenshan97 panicle, score: 92.66 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)
vg1215507555 G C -0.12 -0.06 -0.04 -0.09 -0.08 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215507555 1.14E-06 1.14E-06 mr1108_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
vg1215507555 7.85E-06 NA mr1110_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
vg1215507555 6.11E-07 1.65E-06 mr1112_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
vg1215507555 4.73E-06 4.73E-06 mr1234_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