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Detailed information for vg1213118008:

Variant ID: vg1213118008 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 13118008
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


TGCTCTGACCCACATGGAGAGAAGCTGGCTCGTTGGAGTAAATTGATTGGCAGATACGGCAGCGTCGGACAGAAGTCGAACAACAGGGTCGGATGTATAG[C/T]
AGTAGTCTTCCAGTCTTCGGCTTGTAGTACTAATTGTAGGAAAAGCGCCAGGATGTGATAGATGAAGTTTCAAAACACACAAGTGATGACAAGCCTCACC

Reverse complement sequence

GGTGAGGCTTGTCATCACTTGTGTGTTTTGAAACTTCATCTATCACATCCTGGCGCTTTTCCTACAATTAGTACTACAAGCCGAAGACTGGAAGACTACT[G/A]
CTATACATCCGACCCTGTTGTTCGACTTCTGTCCGACGCTGCCGTATCTGCCAATCAATTTACTCCAACGAGCCAGCTTCTCTCCATGTGGGTCAGAGCA

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 68.20% 31.80% 0.04% 0.00% NA
All Indica  2759 47.30% 52.70% 0.07% 0.00% NA
All Japonica  1512 98.80% 1.20% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 16.60% 83.40% 0.00% 0.00% NA
Indica II  465 73.30% 26.70% 0.00% 0.00% NA
Indica III  913 45.70% 54.10% 0.22% 0.00% NA
Indica Intermediate  786 56.90% 43.10% 0.00% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 98.60% 1.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 86.50% 13.50% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg1213118008 C -> T LOC_Os12g23190.1 downstream_gene_variant ; 3849.0bp to feature; MODIFIER silent_mutation Average:84.919; most accessible tissue: Minghui63 flag leaf, score: 96.434 N N N N
vg1213118008 C -> T LOC_Os12g23200.1 downstream_gene_variant ; 652.0bp to feature; MODIFIER silent_mutation Average:84.919; most accessible tissue: Minghui63 flag leaf, score: 96.434 N N N N
vg1213118008 C -> T LOC_Os12g23210.1 downstream_gene_variant ; 2409.0bp to feature; MODIFIER silent_mutation Average:84.919; most accessible tissue: Minghui63 flag leaf, score: 96.434 N N N N
vg1213118008 C -> T LOC_Os12g23200.2 downstream_gene_variant ; 652.0bp to feature; MODIFIER silent_mutation Average:84.919; most accessible tissue: Minghui63 flag leaf, score: 96.434 N N N N
vg1213118008 C -> T LOC_Os12g23200-LOC_Os12g23210 intergenic_region ; MODIFIER silent_mutation Average:84.919; most accessible tissue: Minghui63 flag leaf, score: 96.434 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)
vg1213118008 C T 0.18 0.01 0.02 0.03 0.08 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1213118008 NA 1.11E-06 mr1308 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
vg1213118008 1.12E-06 NA mr1853 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
vg1213118008 1.96E-07 1.96E-07 mr1853 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
vg1213118008 NA 5.15E-06 mr1308_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
vg1213118008 NA 7.21E-06 mr1361_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
vg1213118008 5.09E-06 5.09E-06 mr1853_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