RiceVarMap2

Search for Variation information by Variation ID:

Detailed information for vg1223100837:

Variant ID: vg1223100837 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23100837
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

CTGTGCCATCTGCTTCGACATGTTCGCCCCCGGTAGGATGAGATCGACGGGGTGCTCCCACAGTCCCACTACAACTGCATCGCTTCGGTGCCCGGACCCC[T/A]
CCTGCTCGGTCGCCGGTGGAGGCGAGCGCGGCGACCTTTCCTGAGGAGGGCGCGGGGGCGGAAGGCGGTGCTGGAGAACAGCCACCGGAGGCCGAGGCAA

Reverse complement sequence

TTGCCTCGGCCTCCGGTGGCTGTTCTCCAGCACCGCCTTCCGCCCCCGCGCCCTCCTCAGGAAAGGTCGCCGCGCTCGCCTCCACCGGCGACCGAGCAGG[A/T]
GGGGTCCGGGCACCGAAGCGATGCAGTTGTAGTGGGACTGTGGGAGCACCCCGTCGATCTCATCCTACCGGGGGCGAACATGTCGAAGCAGATGGCACAG

Allele Frequencies:

Search:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.40%	5.40%	2.14%	5.08%	NA
All Indica	2759	79.80%	8.80%	3.08%	8.26%	NA
All Japonica	1512	98.10%	0.30%	0.93%	0.73%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	96.60%	0.30%	3.03%	0.00%	NA
Indica II	465	32.70%	26.90%	7.96%	32.47%	NA
Indica III	913	96.10%	3.10%	0.11%	0.77%	NA
Indica Intermediate	786	76.10%	11.30%	3.69%	8.91%	NA
Temperate Japonica	767	96.90%	0.30%	1.43%	1.43%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	0.40%	1.24%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	0.00%	1.11%	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
vg1223100837	T -> DEL	N	N	silent_mutation	Average:89.951; most accessible tissue: Minghui63 panicle, score: 97.302	N	N	N	N
vg1223100837	T -> A	LOC_Os12g37610.1	upstream_gene_variant ; 1470.0bp to feature; MODIFIER	silent_mutation	Average:89.951; most accessible tissue: Minghui63 panicle, score: 97.302	N	N	N	N
vg1223100837	T -> A	LOC_Os12g37630.1	upstream_gene_variant ; 1183.0bp to feature; MODIFIER	silent_mutation	Average:89.951; most accessible tissue: Minghui63 panicle, score: 97.302	N	N	N	N
vg1223100837	T -> A	LOC_Os12g37630.2	upstream_gene_variant ; 1183.0bp to feature; MODIFIER	silent_mutation	Average:89.951; most accessible tissue: Minghui63 panicle, score: 97.302	N	N	N	N
vg1223100837	T -> A	LOC_Os12g37620.1	intron_variant ; MODIFIER	silent_mutation	Average:89.951; most accessible tissue: Minghui63 panicle, score: 97.302	N	N	N	N

Showing 1 to 5 of 5 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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Var ID	Ref	Alt	Root (RT)	Young Leaf (YL)	Flag Leaf (FL)	Young Panicle (YP)	Lemma & Palea (LP)	Stamen & Pistil (SP)
vg1223100837	T	A	-0.01	-0.01	-0.02	0.0	-0.01	-0.01

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
vg1223100837	7.80E-06	NA	mr1187_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
vg1223100837	4.09E-06	4.09E-06	mr1187_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

Showing 1 to 2 of 2 entries

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Search for Variation information by Variation ID:

Detailed information for vg1223100837:

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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