Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg1119158633:

Variant ID: vg1119158633 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19158633
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, T: 0.09, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

GCTGGGCTCGGTGCAGTCGACCGCGAGCGATGGGCGCTGCCCCCAGCCACCCCGCGGGCGCACAAGGTGCCGTCTCCTGGCGGCACGCGCGAGGGAGACA[A/T]
ACAACGCCTGCGCGAGGGAGTCAATGCGAGGGGGTTCAGGCGAGGCTGGCGGCGAGGCTCGCACCGCGGCGGCTCCTCTCCTCCGGTGGCAAGGTGCTCG

Reverse complement sequence

CGAGCACCTTGCCACCGGAGGAGAGGAGCCGCCGCGGTGCGAGCCTCGCCGCCAGCCTCGCCTGAACCCCCTCGCATTGACTCCCTCGCGCAGGCGTTGT[T/A]
TGTCTCCCTCGCGCGTGCCGCCAGGAGACGGCACCTTGTGCGCCCGCGGGGTGGCTGGGGGCAGCGCCCATCGCTCGCGGTCGACTGCACCGAGCCCAGC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.90%	3.00%	0.57%	49.56%	NA
All Indica	2759	23.60%	4.90%	0.76%	70.75%	NA
All Japonica	1512	90.50%	0.10%	0.20%	9.26%	NA
Aus	269	29.70%	0.40%	0.00%	69.89%	NA
Indica I	595	59.50%	1.50%	0.50%	38.49%	NA
Indica II	465	4.90%	6.50%	0.65%	87.96%	NA
Indica III	913	11.70%	4.60%	0.88%	82.80%	NA
Indica Intermediate	786	21.10%	7.00%	0.89%	70.99%	NA
Temperate Japonica	767	94.00%	0.10%	0.13%	5.74%	NA
Tropical Japonica	504	87.50%	0.00%	0.20%	12.30%	NA
Japonica Intermediate	241	85.50%	0.00%	0.41%	14.11%	NA
VI/Aromatic	96	81.20%	0.00%	0.00%	18.75%	NA
Intermediate	90	45.60%	2.20%	3.33%	48.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119158633	A -> T	LOC_Os11g32440.1	downstream_gene_variant ; 4761.0bp to feature; MODIFIER	silent_mutation	Average:56.271; most accessible tissue: Minghui63 panicle, score: 95.083	N	N	N	N
vg1119158633	A -> T	LOC_Os11g32460.1	downstream_gene_variant ; 3604.0bp to feature; MODIFIER	silent_mutation	Average:56.271; most accessible tissue: Minghui63 panicle, score: 95.083	N	N	N	N
vg1119158633	A -> T	LOC_Os11g32440-LOC_Os11g32460	intergenic_region ; MODIFIER	silent_mutation	Average:56.271; most accessible tissue: Minghui63 panicle, score: 95.083	N	N	N	N
vg1119158633	A -> DEL	N	N	silent_mutation	Average:56.271; most accessible tissue: Minghui63 panicle, score: 95.083	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)
vg1119158633	A	T	0.0	0.0	0.0	0.0	0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119158633	NA	1.34E-07	mr1354	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
vg1119158633	NA	2.88E-06	mr1138_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
vg1119158633	2.08E-06	2.20E-10	mr1354_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