Search for Variation information by Variation ID:

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

Detailed information for vg0821794641:

Variant ID: vg0821794641 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21794641
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCACACACATGTATGTGGCCGGTGAATGTAAACTCAACTAATTAATTACTTGCCTTGTTGCGCGTACCACTGCTGGGGAAGCACATCACACACTTTGTT[A/T]
AGTTATGAGAGATTGATTATATATCCCTTTGGATAGGATTATGTTTAGTTGGGTGGTGGTCCATGTAACTATCATAGTTAATGGTGGGGCTTAAAATAAG

Reverse complement sequence

CTTATTTTAAGCCCCACCATTAACTATGATAGTTACATGGACCACCACCCAACTAAACATAATCCTATCCAAAGGGATATATAATCAATCTCTCATAACT[T/A]
AACAAAGTGTGTGATGTGCTTCCCCAGCAGTGGTACGCGCAACAAGGCAAGTAATTAATTAGTTGAGTTTACATTCACCGGCCACATACATGTGTGTGCC

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	63.20%	0.30%	21.71%	14.73%	NA
All Indica	2759	49.80%	0.40%	33.13%	16.64%	NA
All Japonica	1512	87.30%	0.10%	2.58%	9.99%	NA
Aus	269	61.00%	0.40%	19.33%	19.33%	NA
Indica I	595	38.20%	1.00%	48.40%	12.44%	NA
Indica II	465	48.80%	0.20%	37.20%	13.76%	NA
Indica III	913	57.40%	0.10%	20.15%	22.34%	NA
Indica Intermediate	786	50.40%	0.50%	34.22%	14.89%	NA
Temperate Japonica	767	98.70%	0.10%	0.65%	0.52%	NA
Tropical Japonica	504	69.60%	0.20%	4.56%	25.60%	NA
Japonica Intermediate	241	88.00%	0.00%	4.56%	7.47%	NA
VI/Aromatic	96	72.90%	0.00%	8.33%	18.75%	NA
Intermediate	90	67.80%	0.00%	14.44%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0821794641	A -> T	LOC_Os08g34690.1	downstream_gene_variant ; 2833.0bp to feature; MODIFIER	silent_mutation	Average:74.317; most accessible tissue: Callus, score: 96.112	N	N	N	N
vg0821794641	A -> T	LOC_Os08g34680-LOC_Os08g34690	intergenic_region ; MODIFIER	silent_mutation	Average:74.317; most accessible tissue: Callus, score: 96.112	N	N	N	N
vg0821794641	A -> DEL	N	N	silent_mutation	Average:74.317; most accessible tissue: Callus, score: 96.112	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)
vg0821794641	A	T	0.07	0.04	0.01	0.0	0.09	0.13

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821794641	NA	2.25E-06	mr1382	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