Search for Variation information by Variation ID:

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

Detailed information for vg0517499780:

Variant ID: vg0517499780 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17499780
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.82, C: 0.19, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TCGGGACTGATTCACTGCCGGCTACTTGCCTGCCTGCTGCATGGAGCGTTGGAGCTGATGATGCTGCAAAATGGCGACGCAGAGGCATTTGTTTTATCCA[T/C]
TGCGTTGGCGTGGCAGCCGCTCGGTCACCATCTGACGGACAGAAACTTATCATGTTGGTTCTTGTATATTATTGTATGGTATGACAAATTACTAGTAGTA

Reverse complement sequence

TACTACTAGTAATTTGTCATACCATACAATAATATACAAGAACCAACATGATAAGTTTCTGTCCGTCAGATGGTGACCGAGCGGCTGCCACGCCAACGCA[A/G]
TGGATAAAACAAATGCCTCTGCGTCGCCATTTTGCAGCATCATCAGCTCCAACGCTCCATGCAGCAGGCAGGCAAGTAGCCGGCAGTGAATCAGTCCCGA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.00%	37.40%	0.17%	0.40%	NA
All Indica	2759	93.10%	6.30%	0.04%	0.54%	NA
All Japonica	1512	9.80%	89.80%	0.26%	0.13%	NA
Aus	269	61.00%	38.30%	0.74%	0.00%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	74.40%	24.70%	0.00%	0.86%	NA
Indica III	913	97.60%	1.90%	0.11%	0.44%	NA
Indica Intermediate	786	94.10%	5.10%	0.00%	0.76%	NA
Temperate Japonica	767	2.70%	97.10%	0.13%	0.00%	NA
Tropical Japonica	504	24.20%	75.40%	0.00%	0.40%	NA
Japonica Intermediate	241	2.10%	96.70%	1.24%	0.00%	NA
VI/Aromatic	96	6.20%	92.70%	0.00%	1.04%	NA
Intermediate	90	47.80%	50.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0517499780	T -> DEL	N	N	silent_mutation	Average:93.319; most accessible tissue: Callus, score: 99.042	N	N	N	N
vg0517499780	T -> C	LOC_Os05g30200.1	upstream_gene_variant ; 2757.0bp to feature; MODIFIER	silent_mutation	Average:93.319; most accessible tissue: Callus, score: 99.042	N	N	N	N
vg0517499780	T -> C	LOC_Os05g30180.1	downstream_gene_variant ; 4114.0bp to feature; MODIFIER	silent_mutation	Average:93.319; most accessible tissue: Callus, score: 99.042	N	N	N	N
vg0517499780	T -> C	LOC_Os05g30190.1	downstream_gene_variant ; 649.0bp to feature; MODIFIER	silent_mutation	Average:93.319; most accessible tissue: Callus, score: 99.042	N	N	N	N
vg0517499780	T -> C	LOC_Os05g30190-LOC_Os05g30200	intergenic_region ; MODIFIER	silent_mutation	Average:93.319; most accessible tissue: Callus, score: 99.042	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)
vg0517499780	T	C	0.02	0.03	0.03	0.01	0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517499780	NA	4.07E-06	mr1002	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
vg0517499780	NA	2.59E-07	mr1044	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
vg0517499780	NA	3.57E-06	mr1044	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
vg0517499780	NA	6.95E-19	mr1077	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
vg0517499780	NA	1.87E-07	mr1399	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
vg0517499780	NA	3.83E-09	mr1827	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
vg0517499780	NA	1.28E-08	mr1002_2	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
vg0517499780	NA	4.39E-06	mr1133_2	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
vg0517499780	NA	9.06E-08	mr1167_2	Ind_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
vg0517499780	NA	8.33E-07	mr1399_2	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
vg0517499780	NA	6.12E-06	mr1726_2	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
vg0517499780	NA	2.87E-13	mr1904_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