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Detailed information for vg1125621218:

Variant ID: vg1125621218 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 25621218
Reference Allele: C	Alternative Allele: CA,T,CAA
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 254. )

Flanking Sequence (100 bp) in Reference Genome:

AAATATAAATATGTACAAAAGAGATGCGAAAATACTAAACTACCCCTAATATCTTAACACGTAGTACAATGCTGAACCAAGTTGATCTGCAAGTCCTTGC[C/CA,T,CAA]
AAAAAACCAAACTTGAAAATTTTTTATAACCATTTAGATGACATGCAAGAAACGGGTGGACGTTCACCCGAGTGTTTAAAACATTTTCCCTCTTGGACAG

Reverse complement sequence

CTGTCCAAGAGGGAAAATGTTTTAAACACTCGGGTGAACGTCCACCCGTTTCTTGCATGTCATCTAAATGGTTATAAAAAATTTTCAAGTTTGGTTTTTT[G/TG,A,TTG]
GCAAGGACTTGCAGATCAACTTGGTTCAGCATTGTACTACGTGTTAAGATATTAGGGGTAGTTTAGTATTTTCGCATCTCTTTTGTACATATTTATATTT

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	68.00%	14.00%	0.47%	0.66%	CA: 13.71%; CAA: 3.09%
All Indica	2759	65.10%	21.80%	0.51%	0.07%	CA: 12.50%
All Japonica	1512	76.20%	0.30%	0.46%	1.92%	CA: 11.90%; CAA: 9.19%
Aus	269	59.10%	16.40%	0.00%	0.00%	CA: 24.54%
Indica I	595	47.40%	9.60%	1.18%	0.00%	CA: 41.85%
Indica II	465	87.30%	10.30%	0.00%	0.00%	CA: 2.37%
Indica III	913	61.20%	35.80%	0.11%	0.22%	CA: 2.63%
Indica Intermediate	786	69.80%	21.60%	0.76%	0.00%	CA: 7.76%
Temperate Japonica	767	79.10%	0.10%	0.39%	0.00%	CAA: 16.95%; CA: 3.39%
Tropical Japonica	504	75.80%	0.40%	0.60%	5.36%	CA: 16.87%; CAA: 0.99%
Japonica Intermediate	241	67.60%	0.80%	0.41%	0.83%	CA: 28.63%; CAA: 1.66%
VI/Aromatic	96	54.20%	0.00%	1.04%	0.00%	CA: 44.79%
Intermediate	90	62.20%	14.40%	0.00%	0.00%	CA: 15.56%; CAA: 7.78%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125621218	C -> T	LOC_Os11g42540.1	downstream_gene_variant ; 3834.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> T	LOC_Os11g42550.1	downstream_gene_variant ; 2514.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> T	LOC_Os11g42540.2	downstream_gene_variant ; 3834.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> T	LOC_Os11g42570.1	intron_variant ; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> DEL	N	N	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> CAA	LOC_Os11g42540.1	downstream_gene_variant ; 3835.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> CAA	LOC_Os11g42550.1	downstream_gene_variant ; 2515.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> CAA	LOC_Os11g42540.2	downstream_gene_variant ; 3835.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> CAA	LOC_Os11g42570.1	intron_variant ; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> CA	LOC_Os11g42540.1	downstream_gene_variant ; 3835.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> CA	LOC_Os11g42550.1	downstream_gene_variant ; 2515.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> CA	LOC_Os11g42540.2	downstream_gene_variant ; 3835.0bp to feature; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	N	N	N	N
vg1125621218	C -> CA	LOC_Os11g42570.1	intron_variant ; MODIFIER	silent_mutation	Average:80.032; most accessible tissue: Zhenshan97 panicle, score: 90.061	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)
vg1125621218	C	CA	-0.04	0.01	0.02	0.02	0.04	0.07
vg1125621218	C	CAA	-0.09	0.04	0.09	0.01	0.05	0.08
vg1125621218	C	T	-0.07	-0.03	-0.02	-0.01	-0.03	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125621218	5.07E-06	NA	mr1662	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
vg1125621218	1.49E-07	3.95E-09	mr1662	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