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Detailed information for vg1118461468:

Variant ID: vg1118461468 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18461468
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TAGGCTAGCTAGCACTGCGGCTACGACAGCAACTGCCTATGGTATGTGTATTTACAAATCTACTTACTCCAGTTTCCCAATGTAAGTCATTCTAATATTT[C/T]
CCACATTTATATTAATGTCAATGAATCTAGATAGATATATATGTCTAGATTTATTAACATCAATATAAATGTGGAAAATGCTAGAATGACTTACATTGTG

Reverse complement sequence

CACAATGTAAGTCATTCTAGCATTTTCCACATTTATATTGATGTTAATAAATCTAGACATATATATCTATCTAGATTCATTGACATTAATATAAATGTGG[G/A]
AAATATTAGAATGACTTACATTGGGAAACTGGAGTAAGTAGATTTGTAAATACACATACCATAGGCAGTTGCTGTCGTAGCCGCAGTGCTAGCTAGCCTA

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 70.20% 29.10% 0.36% 0.40% NA
All Indica  2759 55.50% 44.20% 0.33% 0.00% NA
All Japonica  1512 94.70% 3.70% 0.40% 1.19% NA
Aus  269 80.70% 19.00% 0.00% 0.37% NA
Indica I  595 74.10% 25.50% 0.34% 0.00% NA
Indica II  465 46.70% 53.30% 0.00% 0.00% NA
Indica III  913 52.10% 47.60% 0.22% 0.00% NA
Indica Intermediate  786 50.40% 49.00% 0.64% 0.00% NA
Temperate Japonica  767 95.70% 1.80% 0.13% 2.35% NA
Tropical Japonica  504 95.80% 3.60% 0.60% 0.00% NA
Japonica Intermediate  241 89.20% 10.00% 0.83% 0.00% NA
VI/Aromatic  96 82.30% 17.70% 0.00% 0.00% NA
Intermediate  90 64.40% 33.30% 2.22% 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
vg1118461468 C -> T LOC_Os11g31590.1 downstream_gene_variant ; 2752.0bp to feature; MODIFIER silent_mutation Average:77.736; most accessible tissue: Callus, score: 96.757 N N N N
vg1118461468 C -> T LOC_Os11g31570-LOC_Os11g31590 intergenic_region ; MODIFIER silent_mutation Average:77.736; most accessible tissue: Callus, score: 96.757 N N N N
vg1118461468 C -> DEL N N silent_mutation Average:77.736; most accessible tissue: Callus, score: 96.757 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)
vg1118461468 C T 0.0 0.01 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1118461468 NA 8.27E-06 mr1064_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
vg1118461468 4.48E-06 NA mr1098_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
vg1118461468 2.53E-06 NA mr1150_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
vg1118461468 NA 9.15E-06 mr1240_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