Search for Variation information by Variation ID:

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Detailed information for vg0401152900:

Variant ID: vg0401152900 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 1152900
Reference Allele: CGCGGAAAACAAGGGTGAGGAGTT	Alternative Allele: TGCGGAAAACAAGGGTGAGGAGTT,C
Primary Allele: CGCGGAAAACAAGGGTGAGG AGTT	Secondary Allele: TGCGGAAAACAAGGGTGAGG AGTT

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTCCCCCCTAAAATGGATCATTATGATTTTTTAAGCAACTTTCGTATATAGATTTTTTTTTAAAAAACACACCGTTTAATAGTTTGAAAAGCATGCG[CGCGGAAAACAAGGGTGAGGAGTT/TGCGGAAAACAAGGGTGAGGAGTT,C]
GAGAACTCCCAGCAAAGAACTGGCCTAAGTTTCTTTCAACTTCACTTATTTTAGTGTGAGATTGTAATAATTGGCTATAACTCTTTGAGCAAAGGCCGGA

Reverse complement sequence

TCCGGCCTTTGCTCAAAGAGTTATAGCCAATTATTACAATCTCACACTAAAATAAGTGAAGTTGAAAGAAACTTAGGCCAGTTCTTTGCTGGGAGTTCTC[AACTCCTCACCCTTGTTTTCCGCG/AACTCCTCACCCTTGTTTTCCGCA,G]
CGCATGCTTTTCAAACTATTAAACGGTGTGTTTTTTAAAAAAAAATCTATATACGAAAGTTGCTTAAAAAATCATAATGATCCATTTTAGGGGGGAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of CGCGGAAAACAAGGGTGAGG AGTT(primary allele)	Frequency of TGCGGAAAACAAGGGTGAGG AGTT(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.70%	38.80%	0.49%	0.00%	C: 0.02%
All Indica	2759	46.20%	52.90%	0.80%	0.00%	C: 0.04%
All Japonica	1512	95.80%	4.20%	0.00%	0.00%	NA
Aus	269	5.60%	94.40%	0.00%	0.00%	NA
Indica I	595	77.80%	22.20%	0.00%	0.00%	NA
Indica II	465	25.80%	70.80%	3.23%	0.00%	C: 0.22%
Indica III	913	40.70%	59.00%	0.22%	0.00%	NA
Indica Intermediate	786	40.80%	58.50%	0.64%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	89.50%	10.50%	0.00%	0.00%	NA
Japonica Intermediate	241	96.70%	3.30%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	54.40%	44.40%	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
vg0401152900	CGCGGAAAACAAGGGTGAGGAGTT -> C	LOC_Os04g02910.1	upstream_gene_variant ; 682.0bp to feature; MODIFIER	silent_mutation	Average:82.166; most accessible tissue: Zhenshan97 flag leaf, score: 92.089	N	N	N	N
vg0401152900	CGCGGAAAACAAGGGTGAGGAGTT -> C	LOC_Os04g02910.3	upstream_gene_variant ; 1474.0bp to feature; MODIFIER	silent_mutation	Average:82.166; most accessible tissue: Zhenshan97 flag leaf, score: 92.089	N	N	N	N
vg0401152900	CGCGGAAAACAAGGGTGAGGAGTT -> C	LOC_Os04g02910.4	upstream_gene_variant ; 682.0bp to feature; MODIFIER	silent_mutation	Average:82.166; most accessible tissue: Zhenshan97 flag leaf, score: 92.089	N	N	N	N
vg0401152900	CGCGGAAAACAAGGGTGAGGAGTT -> C	LOC_Os04g02910-LOC_Os04g02920	intergenic_region ; MODIFIER	silent_mutation	Average:82.166; most accessible tissue: Zhenshan97 flag leaf, score: 92.089	N	N	N	N
vg0401152900	CGCGGAAAACAAGGGTGAGGAGTT -> TGCGGAAAACAAGGGTGAGGAGTT	LOC_Os04g02910.1	upstream_gene_variant ; 681.0bp to feature; MODIFIER	silent_mutation	Average:82.166; most accessible tissue: Zhenshan97 flag leaf, score: 92.089	N	N	N	N
vg0401152900	CGCGGAAAACAAGGGTGAGGAGTT -> TGCGGAAAACAAGGGTGAGGAGTT	LOC_Os04g02910.3	upstream_gene_variant ; 1473.0bp to feature; MODIFIER	silent_mutation	Average:82.166; most accessible tissue: Zhenshan97 flag leaf, score: 92.089	N	N	N	N
vg0401152900	CGCGGAAAACAAGGGTGAGGAGTT -> TGCGGAAAACAAGGGTGAGGAGTT	LOC_Os04g02910.4	upstream_gene_variant ; 681.0bp to feature; MODIFIER	silent_mutation	Average:82.166; most accessible tissue: Zhenshan97 flag leaf, score: 92.089	N	N	N	N
vg0401152900	CGCGGAAAACAAGGGTGAGGAGTT -> TGCGGAAAACAAGGGTGAGGAGTT	LOC_Os04g02910-LOC_Os04g02920	intergenic_region ; MODIFIER	silent_mutation	Average:82.166; most accessible tissue: Zhenshan97 flag leaf, score: 92.089	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)
vg0401152900	CGCGG*	C	0.03	0.13	0.21	0.06	0.13	0.07
vg0401152900	CGCGG*	TGCGG*	0.0	0.0	0.0	-0.02	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401152900	NA	3.30E-09	mr1108	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
vg0401152900	NA	1.35E-06	mr1111	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
vg0401152900	NA	6.59E-06	mr1200	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
vg0401152900	NA	6.66E-10	mr1565	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
vg0401152900	NA	3.75E-09	mr1565	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
vg0401152900	3.76E-06	NA	mr1878	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
vg0401152900	3.78E-08	1.37E-08	mr1878	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