Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0816725186:

Variant ID: vg0816725186 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16725186
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTTTTTTTAATAAGACTTAGACTAGTTTCTTTTTTCCTTTTTAAGAACAACAATAATCATACATGGTTTGACTTTTTTCCAATTTACTGTCTTGACTTT[A/G]
TACGATAAAAAACTTTATGTACTCCCTCCGTTTCGAAATGTTTGACACCGTTGATTTTTTAGCACATGTTTAACCGTTCGTCTTATTCAAAAACTTTTGT

Reverse complement sequence

ACAAAAGTTTTTGAATAAGACGAACGGTTAAACATGTGCTAAAAAATCAACGGTGTCAAACATTTCGAAACGGAGGGAGTACATAAAGTTTTTTATCGTA[T/C]
AAAGTCAAGACAGTAAATTGGAAAAAAGTCAAACCATGTATGATTATTGTTGTTCTTAAAAAGGAAAAAAGAAACTAGTCTAAGTCTTATTAAAAAAAGT

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	94.50%	0.80%	1.27%	3.45%	NA
All Indica	2759	98.50%	0.00%	0.07%	1.41%	NA
All Japonica	1512	89.20%	2.60%	3.70%	4.50%	NA
Aus	269	82.20%	0.00%	0.00%	17.84%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	98.90%	0.00%	0.00%	1.10%	NA
Indica Intermediate	786	96.20%	0.00%	0.13%	3.69%	NA
Temperate Japonica	767	89.60%	4.00%	6.13%	0.26%	NA
Tropical Japonica	504	88.10%	0.00%	0.20%	11.71%	NA
Japonica Intermediate	241	90.50%	3.30%	3.32%	2.90%	NA
VI/Aromatic	96	95.80%	0.00%	1.04%	3.12%	NA
Intermediate	90	93.30%	0.00%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816725186	A -> G	LOC_Os08g27400.1	upstream_gene_variant ; 1578.0bp to feature; MODIFIER	silent_mutation	Average:76.497; most accessible tissue: Minghui63 panicle, score: 88.595	N	N	N	N
vg0816725186	A -> G	LOC_Os08g27410.1	upstream_gene_variant ; 4055.0bp to feature; MODIFIER	silent_mutation	Average:76.497; most accessible tissue: Minghui63 panicle, score: 88.595	N	N	N	N
vg0816725186	A -> G	LOC_Os08g27390.1	downstream_gene_variant ; 3881.0bp to feature; MODIFIER	silent_mutation	Average:76.497; most accessible tissue: Minghui63 panicle, score: 88.595	N	N	N	N
vg0816725186	A -> G	LOC_Os08g27400-LOC_Os08g27410	intergenic_region ; MODIFIER	silent_mutation	Average:76.497; most accessible tissue: Minghui63 panicle, score: 88.595	N	N	N	N
vg0816725186	A -> DEL	N	N	silent_mutation	Average:76.497; most accessible tissue: Minghui63 panicle, score: 88.595	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)
vg0816725186	A	G	0.01	0.0	0.0	0.0	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816725186	NA	5.69E-06	mr1210	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
vg0816725186	1.64E-06	1.64E-06	mr1409	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
vg0816725186	4.02E-06	NA	mr1410	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