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Detailed information for vg1215337617:

Variant ID: vg1215337617 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 15337617
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


GTTTGTATCTGACTCCTAAATAGTGATCATTGCCAGTTGGCGTTCGTGGTTTTTTCCCGACGTAAAATTCCGTGTCTGCGTTATGTATCTATTTTCTTAA[C/T]
GAGTGGTATCAGAGCATTGGAGATTCGATCTACACGACGTGGTCGTTTTTCTTTCTGCAATCCCTGCCATCGGTGCGATTTCTCGGATCGAAGAGTCGAT

Reverse complement sequence

ATCGACTCTTCGATCCGAGAAATCGCACCGATGGCAGGGATTGCAGAAAGAAAAACGACCACGTCGTGTAGATCGAATCTCCAATGCTCTGATACCACTC[G/A]
TTAAGAAAATAGATACATAACGCAGACACGGAATTTTACGTCGGGAAAAAACCACGAACGCCAACTGGCAATGATCACTATTTAGGAGTCAGATACAAAC

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 77.30% 22.70% 0.06% 0.00% NA
All Indica  2759 75.80% 24.20% 0.07% 0.00% NA
All Japonica  1512 79.40% 20.60% 0.00% 0.00% NA
Aus  269 91.40% 8.60% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 45.80% 54.20% 0.00% 0.00% NA
Indica III  913 80.20% 19.60% 0.22% 0.00% NA
Indica Intermediate  786 72.60% 27.40% 0.00% 0.00% NA
Temperate Japonica  767 95.20% 4.80% 0.00% 0.00% NA
Tropical Japonica  504 56.20% 43.80% 0.00% 0.00% NA
Japonica Intermediate  241 78.00% 22.00% 0.00% 0.00% NA
VI/Aromatic  96 46.90% 53.10% 0.00% 0.00% NA
Intermediate  90 77.80% 21.10% 1.11% 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
vg1215337617 C -> T LOC_Os12g26290.1 intron_variant ; MODIFIER silent_mutation Average:81.069; most accessible tissue: Minghui63 young leaf, score: 98.896 N N N N
vg1215337617 C -> T LOC_Os12g26290.2 intron_variant ; MODIFIER silent_mutation Average:81.069; most accessible tissue: Minghui63 young leaf, score: 98.896 N N N N
vg1215337617 C -> T LOC_Os12g26290.3 intron_variant ; MODIFIER silent_mutation Average:81.069; most accessible tissue: Minghui63 young leaf, score: 98.896 N N N N
vg1215337617 C -> T LOC_Os12g26290.4 intron_variant ; MODIFIER silent_mutation Average:81.069; most accessible tissue: Minghui63 young leaf, score: 98.896 N N N N
vg1215337617 C -> T LOC_Os12g26290.5 intron_variant ; MODIFIER silent_mutation Average:81.069; most accessible tissue: Minghui63 young leaf, score: 98.896 N N N N
vg1215337617 C -> T LOC_Os12g26290.6 intron_variant ; MODIFIER silent_mutation Average:81.069; most accessible tissue: Minghui63 young leaf, score: 98.896 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)
vg1215337617 C T -0.09 -0.2 -0.19 -0.03 -0.11 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1215337617 NA 2.46E-11 mr1024_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
vg1215337617 NA 5.81E-07 mr1169_2 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