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Detailed information for vg0806011712:

Variant ID: vg0806011712 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6011712
Reference Allele: A	Alternative Allele: G,C
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCATGATGGTAACATGCTAATTACCTTTATGTTTAACATACTCCATTCATCTTAAAAAAATAACCTAAAATTAAGATCAATTTTACGGACCTTGAGGAG[A/G,C]
TACCATGAGGTACCATTTTTTCTATTGTAAATTTGGTACCTCGTGGTACCTAGGTACTATGAGGTGGTACCAAATTTTACACTAAAATTTTGGTACCTCA

Reverse complement sequence

TGAGGTACCAAAATTTTAGTGTAAAATTTGGTACCACCTCATAGTACCTAGGTACCACGAGGTACCAAATTTACAATAGAAAAAATGGTACCTCATGGTA[T/C,G]
CTCCTCAAGGTCCGTAAAATTGATCTTAATTTTAGGTTATTTTTTTAAGATGAATGGAGTATGTTAAACATAAAGGTAATTAGCATGTTACCATCATGGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.80%	18.50%	0.89%	10.73%	C: 0.02%
All Indica	2759	72.70%	11.90%	0.54%	14.90%	C: 0.04%
All Japonica	1512	63.20%	34.50%	1.59%	0.73%	NA
Aus	269	71.40%	3.70%	1.12%	23.79%	NA
Indica I	595	97.60%	0.30%	0.17%	1.85%	NA
Indica II	465	61.10%	7.10%	0.86%	30.97%	NA
Indica III	913	59.70%	22.70%	0.77%	16.76%	C: 0.11%
Indica Intermediate	786	75.70%	10.80%	0.38%	13.10%	NA
Temperate Japonica	767	62.20%	35.50%	2.35%	0.00%	NA
Tropical Japonica	504	69.00%	29.00%	0.79%	1.19%	NA
Japonica Intermediate	241	54.40%	42.70%	0.83%	2.07%	NA
VI/Aromatic	96	82.30%	3.10%	0.00%	14.58%	NA
Intermediate	90	75.60%	16.70%	0.00%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806011712	A -> G	LOC_Os08g10304.1	upstream_gene_variant ; 4638.0bp to feature; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> G	LOC_Os08g10310.1	upstream_gene_variant ; 4033.0bp to feature; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> G	LOC_Os08g10310.2	upstream_gene_variant ; 4033.0bp to feature; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> G	LOC_Os08g10310.3	upstream_gene_variant ; 4033.0bp to feature; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> G	LOC_Os08g10304-LOC_Os08g10310	intergenic_region ; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> C	LOC_Os08g10304.1	upstream_gene_variant ; 4638.0bp to feature; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> C	LOC_Os08g10310.1	upstream_gene_variant ; 4033.0bp to feature; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> C	LOC_Os08g10310.2	upstream_gene_variant ; 4033.0bp to feature; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> C	LOC_Os08g10310.3	upstream_gene_variant ; 4033.0bp to feature; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> C	LOC_Os08g10304-LOC_Os08g10310	intergenic_region ; MODIFIER	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	N	N	N	N
vg0806011712	A -> DEL	N	N	silent_mutation	Average:50.131; most accessible tissue: Callus, score: 95.2	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)
vg0806011712	A	C	0.04	0.02	0.01	0.02	0.01	-0.01
vg0806011712	A	G	-0.01	-0.01	-0.01	0.03	0.0	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806011712	3.82E-06	9.57E-06	mr1186	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
vg0806011712	NA	9.10E-07	mr1186	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
vg0806011712	5.96E-07	5.96E-07	mr1197	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
vg0806011712	NA	2.66E-06	mr1482	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
vg0806011712	NA	2.49E-06	mr1622	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
vg0806011712	NA	8.09E-06	mr1958	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