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Detailed information for vg1203938514:

Variant ID: vg1203938514 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3938514
Reference Allele: T	Alternative Allele: C,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGAAGGCGGCGGCTTCCTCCGCGACTGCGGCTGCGCCCACGCCGTCGCCGGCTCGCCGCCGTCGGCAGTTGAGGCGAGCCCGGCACGACGCCAGTGCGC[T/C,G]
GCCGCTATCTTTGTCCTCCGCCGCTTGCTCGCATGGGCGGCGCTGTCTCCATCCGGCCAGCACCGTCTCACGGCGGCGCCGCGTTTGTGGGGGGAATGGG

Reverse complement sequence

CCCATTCCCCCCACAAACGCGGCGCCGCCGTGAGACGGTGCTGGCCGGATGGAGACAGCGCCGCCCATGCGAGCAAGCGGCGGAGGACAAAGATAGCGGC[A/G,C]
GCGCACTGGCGTCGTGCCGGGCTCGCCTCAACTGCCGACGGCGGCGAGCCGGCGACGGCGTGGGCGCAGCCGCAGTCGCGGAGGAAGCCGCCGCCTTCGC

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	66.90%	32.40%	0.17%	0.00%	G: 0.44%
All Indica	2759	97.00%	2.10%	0.22%	0.00%	G: 0.76%
All Japonica	1512	11.80%	88.10%	0.13%	0.00%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	99.30%	0.30%	0.34%	0.00%	NA
Indica II	465	97.80%	1.90%	0.22%	0.00%	NA
Indica III	913	95.60%	2.10%	0.11%	0.00%	G: 2.19%
Indica Intermediate	786	96.20%	3.40%	0.25%	0.00%	G: 0.13%
Temperate Japonica	767	1.40%	98.40%	0.13%	0.00%	NA
Tropical Japonica	504	22.20%	77.60%	0.20%	0.00%	NA
Japonica Intermediate	241	22.80%	77.20%	0.00%	0.00%	NA
VI/Aromatic	96	22.90%	77.10%	0.00%	0.00%	NA
Intermediate	90	41.10%	58.90%	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
vg1203938514	T -> C	LOC_Os12g07790.1	upstream_gene_variant ; 422.0bp to feature; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> C	LOC_Os12g07800.1	upstream_gene_variant ; 368.0bp to feature; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> C	LOC_Os12g07780.1	downstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> C	LOC_Os12g07780.2	downstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> C	LOC_Os12g07790-LOC_Os12g07800	intergenic_region ; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> G	LOC_Os12g07790.1	upstream_gene_variant ; 422.0bp to feature; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> G	LOC_Os12g07800.1	upstream_gene_variant ; 368.0bp to feature; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> G	LOC_Os12g07780.1	downstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> G	LOC_Os12g07780.2	downstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	N	N	N	N
vg1203938514	T -> G	LOC_Os12g07790-LOC_Os12g07800	intergenic_region ; MODIFIER	silent_mutation	Average:96.45; most accessible tissue: Zhenshan97 panicle, score: 98.337	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)
vg1203938514	T	C	-0.03	-0.03	-0.03	-0.03	-0.04	-0.04
vg1203938514	T	G	-0.02	-0.03	-0.02	-0.02	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203938514	NA	5.88E-12	mr1386	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
vg1203938514	NA	2.50E-27	mr1414	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
vg1203938514	NA	7.66E-23	mr1386_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
vg1203938514	NA	7.11E-35	mr1448_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
vg1203938514	4.73E-06	4.73E-06	mr1448_2	Jap_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