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Detailed information for vg0528097164:

Variant ID: vg0528097164 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 28097164
Reference Allele: G	Alternative Allele: A,GCAAA
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.06, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CAGCCGGGTGAAAACGGAATCAGAATCAGTAGCATCTCTTTAGAAACGACGATCAACCGGTAATTGATTATATTTACCATTTTAACTACTACTAAGTATT[G/A,GCAAA]
ATATTAATATGATAAAAAAGATATTAGAAAAAAATAAAATGTAAAAATAAAAAAAATGATATGGTTAAAAACGGTACCTAATATAAAAAATAGTGATTGA

Reverse complement sequence

TCAATCACTATTTTTTATATTAGGTACCGTTTTTAACCATATCATTTTTTTTATTTTTACATTTTATTTTTTTCTAATATCTTTTTTATCATATTAATAT[C/T,TTTGC]
AATACTTAGTAGTAGTTAAAATGGTAAATATAATCAATTACCGGTTGATCGTCGTTTCTAAAGAGATGCTACTGATTCTGATTCCGTTTTCACCCGGCTG

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	85.90%	13.90%	0.17%	0.02%	GCAAA: 0.02%
All Indica	2759	81.60%	18.20%	0.18%	0.04%	NA
All Japonica	1512	99.70%	0.20%	0.13%	0.00%	NA
Aus	269	47.20%	52.40%	0.00%	0.00%	GCAAA: 0.37%
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	66.00%	33.50%	0.22%	0.22%	NA
Indica III	913	80.60%	19.20%	0.22%	0.00%	NA
Indica Intermediate	786	78.50%	21.20%	0.25%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.20%	0.40%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	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
vg0528097164	G -> DEL	N	N	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> GCAAA	LOC_Os05g48980.1	upstream_gene_variant ; 2585.0bp to feature; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> GCAAA	LOC_Os05g48990.1	upstream_gene_variant ; 3130.0bp to feature; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> GCAAA	LOC_Os05g48970.1	downstream_gene_variant ; 4737.0bp to feature; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> GCAAA	LOC_Os05g48970.2	downstream_gene_variant ; 4737.0bp to feature; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> GCAAA	LOC_Os05g48980-LOC_Os05g48990	intergenic_region ; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> A	LOC_Os05g48980.1	upstream_gene_variant ; 2584.0bp to feature; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> A	LOC_Os05g48990.1	upstream_gene_variant ; 3131.0bp to feature; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> A	LOC_Os05g48970.1	downstream_gene_variant ; 4736.0bp to feature; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> A	LOC_Os05g48970.2	downstream_gene_variant ; 4736.0bp to feature; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	N	N	N	N
vg0528097164	G -> A	LOC_Os05g48980-LOC_Os05g48990	intergenic_region ; MODIFIER	silent_mutation	Average:87.053; most accessible tissue: Zhenshan97 panicle, score: 97.445	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)
vg0528097164	G	A	0.03	0.03	0.01	-0.01	-0.01	0.02
vg0528097164	G	GCAAA	-0.18	-0.14	-0.26	-0.06	0.01	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0528097164	NA	5.22E-06	mr1904	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
vg0528097164	NA	8.40E-06	mr1720_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
vg0528097164	NA	5.15E-07	mr1733_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
vg0528097164	1.81E-06	NA	mr1762_2	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
vg0528097164	NA	3.71E-06	mr1931_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
vg0528097164	NA	1.01E-06	mr1931_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