Search for Variation information by Variation ID:

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

Detailed information for vg1204217058:

Variant ID: vg1204217058 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4217058
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.10, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

CAAATCGTTTCCTGATGCATCTGTCACCAGACCTCCAGCTTCTGAAAACAGCACAAGCAGAATATCAATCTAAAATGTTTCAGTTGGTTTCTACGTTTTA[G/A]
CACAAGCAGAATATCAATCTAAAATGTTTCAGTTGGGTTCTATGTTTTTTTTCAGGTTGTTGGGTTCTATGTTTTCAATGTTCAAAAAGAGAACCTTCAT

Reverse complement sequence

ATGAAGGTTCTCTTTTTGAACATTGAAAACATAGAACCCAACAACCTGAAAAAAAACATAGAACCCAACTGAAACATTTTAGATTGATATTCTGCTTGTG[C/T]
TAAAACGTAGAAACCAACTGAAACATTTTAGATTGATATTCTGCTTGTGCTGTTTTCAGAAGCTGGAGGTCTGGTGACAGATGCATCAGGAAACGATTTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.80%	21.10%	0.08%	0.00%	NA
All Indica	2759	87.40%	12.40%	0.14%	0.00%	NA
All Japonica	1512	70.40%	29.60%	0.00%	0.00%	NA
Aus	269	62.50%	37.50%	0.00%	0.00%	NA
Indica I	595	92.10%	7.90%	0.00%	0.00%	NA
Indica II	465	80.40%	19.60%	0.00%	0.00%	NA
Indica III	913	88.90%	11.10%	0.00%	0.00%	NA
Indica Intermediate	786	86.30%	13.20%	0.51%	0.00%	NA
Temperate Japonica	767	86.00%	14.00%	0.00%	0.00%	NA
Tropical Japonica	504	55.40%	44.60%	0.00%	0.00%	NA
Japonica Intermediate	241	52.30%	47.70%	0.00%	0.00%	NA
VI/Aromatic	96	12.50%	87.50%	0.00%	0.00%	NA
Intermediate	90	74.40%	25.60%	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
vg1204217058	G -> A	LOC_Os12g08270.1	upstream_gene_variant ; 705.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08260.1	downstream_gene_variant ; 3583.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08290.1	downstream_gene_variant ; 3620.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08260.4	downstream_gene_variant ; 3583.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08260.6	downstream_gene_variant ; 3583.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08260.7	downstream_gene_variant ; 3583.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08260.2	downstream_gene_variant ; 3583.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08260.5	downstream_gene_variant ; 3583.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08260.3	downstream_gene_variant ; 3583.0bp to feature; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	N	N	N	N
vg1204217058	G -> A	LOC_Os12g08280.1	intron_variant ; MODIFIER	silent_mutation	Average:78.193; most accessible tissue: Zhenshan97 root, score: 89.659	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)
vg1204217058	G	A	0.01	0.0	-0.01	-0.01	-0.01	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204217058	NA	2.18E-06	mr1180	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
vg1204217058	NA	1.87E-08	mr1180_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
vg1204217058	NA	1.87E-07	mr1183_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