Search for Variation information by Variation ID:

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

Detailed information for vg0728679937:

Variant ID: vg0728679937 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 28679937
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.88, A: 0.11, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGTTTCATCAGCAAGTGCACGGAACAGACTAGAGAGTGTAGGTGTATGCATGTGTGATGTCATGTAACGAGTTGCCATGCAAAGGCATGAGGATTACG[G/A]
ACCTCTCTTTCGTCGTAATCCTAGCAGCTACAGATTTCAACTGTCGTGTTAACCAAGTGAAGTGCTAGTTTCGAATGTATTGGCCCCTCTCTGCTCTTCT

Reverse complement sequence

AGAAGAGCAGAGAGGGGCCAATACATTCGAAACTAGCACTTCACTTGGTTAACACGACAGTTGAAATCTGTAGCTGCTAGGATTACGACGAAAGAGAGGT[C/T]
CGTAATCCTCATGCCTTTGCATGGCAACTCGTTACATGACATCACACATGCATACACCTACACTCTCTAGTCTGTTCCGTGCACTTGCTGATGAAACCAT

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	60.90%	38.80%	0.02%	0.25%	NA
All Indica	2759	94.30%	5.30%	0.04%	0.40%	NA
All Japonica	1512	0.90%	99.00%	0.00%	0.07%	NA
Aus	269	82.90%	17.10%	0.00%	0.00%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	95.70%	3.90%	0.00%	0.43%	NA
Indica III	913	94.90%	4.90%	0.00%	0.22%	NA
Indica Intermediate	786	88.80%	10.30%	0.13%	0.76%	NA
Temperate Japonica	767	1.00%	99.00%	0.00%	0.00%	NA
Tropical Japonica	504	0.80%	99.00%	0.00%	0.20%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	38.90%	61.10%	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
vg0728679937	G -> DEL	N	N	silent_mutation	Average:82.857; most accessible tissue: Zhenshan97 panicle, score: 89.143	N	N	N	N
vg0728679937	G -> A	LOC_Os07g48030.1	3_prime_UTR_variant ; 207.0bp to feature; MODIFIER	silent_mutation	Average:82.857; most accessible tissue: Zhenshan97 panicle, score: 89.143	N	N	N	N
vg0728679937	G -> A	LOC_Os07g48040.1	upstream_gene_variant ; 4181.0bp to feature; MODIFIER	silent_mutation	Average:82.857; most accessible tissue: Zhenshan97 panicle, score: 89.143	N	N	N	N
vg0728679937	G -> A	LOC_Os07g48020.1	downstream_gene_variant ; 4504.0bp to feature; MODIFIER	silent_mutation	Average:82.857; most accessible tissue: Zhenshan97 panicle, score: 89.143	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)
vg0728679937	G	A	-0.11	-0.05	-0.04	-0.13	-0.15	-0.13

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0728679937	NA	1.24E-25	mr1039	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
vg0728679937	NA	3.87E-09	mr1336	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
vg0728679937	NA	6.37E-13	mr1701	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
vg0728679937	NA	2.87E-18	mr1336_2	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
vg0728679937	NA	1.43E-31	mr1632_2	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
vg0728679937	NA	3.43E-06	mr1915_2	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