RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg0202633802:

Variant ID: vg0202633802 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 2633802
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTACACATCTTAATTCGTTTGGCACTACAGTGACAACAAACCATACCATAGGACATGCATATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATGCAAA[T/G]
TGCTGCTAATATAATGCCTAGCTACAAATATCTCCTAGGTAGAGGGACAAATTCATATCCAAATCGTGTCCTTTGGATAAAGTCCCTAGTAGTACATGAG

Reverse complement sequence

CTCATGTACTACTAGGGACTTTATCCAAAGGACACGATTTGGATATGAATTTGTCCCTCTACCTAGGAGATATTTGTAGCTAGGCATTATATTAGCAGCA[A/C]
TTTGCATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATATGCATGTCCTATGGTATGGTTTGTTGTCACTGTAGTGCCAAACGAATTAAGATGTGTAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.30%	4.40%	1.38%	0.00%	NA
All Indica	2759	99.70%	0.10%	0.18%	0.00%	NA
All Japonica	1512	82.90%	13.20%	3.90%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.50%	0.00%	0.50%	0.00%	NA
Indica II	465	99.40%	0.20%	0.43%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	71.10%	21.90%	7.04%	0.00%	NA
Tropical Japonica	504	95.20%	4.40%	0.40%	0.00%	NA
Japonica Intermediate	241	95.00%	3.70%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	1.11%	0.00%	NA

Showing 1 to 13 of 13 entries

Allele Effect:

Search:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0202633802	T -> G	LOC_Os02g05460.1	upstream_gene_variant ; 1691.0bp to feature; MODIFIER	silent_mutation	Average:73.94; most accessible tissue: Minghui63 flag leaf, score: 94.364	N	N	N	N
vg0202633802	T -> G	LOC_Os02g05470.1	upstream_gene_variant ; 4615.0bp to feature; MODIFIER	silent_mutation	Average:73.94; most accessible tissue: Minghui63 flag leaf, score: 94.364	N	N	N	N
vg0202633802	T -> G	LOC_Os02g05470.2	upstream_gene_variant ; 4615.0bp to feature; MODIFIER	silent_mutation	Average:73.94; most accessible tissue: Minghui63 flag leaf, score: 94.364	N	N	N	N
vg0202633802	T -> G	LOC_Os02g05460-LOC_Os02g05470	intergenic_region ; MODIFIER	silent_mutation	Average:73.94; most accessible tissue: Minghui63 flag leaf, score: 94.364	N	N	N	N

Showing 1 to 4 of 4 entries

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.

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Search:

Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg0202633802	T	G	0.03	0.01	-0.02	0.18	0.13	0.13

Showing 1 to 1 of 1 entries

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Putative Genotype-Phenotype Associations:

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Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0202633802	5.51E-07	NA	mr1238	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
vg0202633802	1.09E-06	NA	mr1484	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
vg0202633802	4.89E-06	NA	mr1841	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
vg0202633802	8.02E-09	NA	mr1768_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
vg0202633802	NA	8.79E-07	mr1768_2	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

Showing 1 to 5 of 5 entries

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Search for Variation information by Variation ID:

Detailed information for vg0202633802:

Flanking Sequence (100 bp) in Reference Genome:

Reverse complement sequence

Allele Frequencies:

Allele Effect:

Effects Predicted by Deep Convolutional Neural Networks

Putative Genotype-Phenotype Associations:

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