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Detailed information for vg1123942722:

Variant ID: vg1123942722 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 23942722
Reference Allele: AGAGAGAG	Alternative Allele: GGAGAGAG,TGAGAGAG,A,AGGAGAGAG
Primary Allele: AGAGAGAG	Secondary Allele: GGAGAGAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTGTTGGCCCGTGAAGGCCCAAATAGGATCCAATAAGAGAGGAGGGCCTCCTGGATTCCGCGTTGCCGCCTTCAATTCCATTCGAACGAAACGAGGAGA[AGAGAGAG/GGAGAGAG,TGAGAGAG,A,AGGAGAGAG]
GAGAGAGGAGAGAGAGGGGTTTGTGTGGCTGCGAGTGGGCCCCATGTCGACGTCGGCGGCGGCGTCGGCGGCGGCGGAGCAGCAGCAGGAGGAGGGGGAG

Reverse complement sequence

CTCCCCCTCCTCCTGCTGCTGCTCCGCCGCCGCCGACGCCGCCGCCGACGTCGACATGGGGCCCACTCGCAGCCACACAAACCCCTCTCTCTCCTCTCTC[CTCTCTCT/CTCTCTCC,CTCTCTCA,T,CTCTCTCCT]
TCTCCTCGTTTCGTTCGAATGGAATTGAAGGCGGCAACGCGGAATCCAGGAGGCCCTCCTCTCTTATTGGATCCTATTTGGGCCTTCACGGGCCAACACG

Allele Frequencies:

Populations	Population Size	Frequency of AGAGAGAG(primary allele)	Frequency of GGAGAGAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.80%	37.70%	6.24%	1.93%	TGAGAGAG: 3.98%; A: 0.34%; AGGAGAGAG: 0.04%
All Indica	2759	50.60%	35.80%	3.81%	3.30%	TGAGAGAG: 6.45%; A: 0.04%
All Japonica	1512	50.60%	38.60%	10.32%	0.00%	TGAGAGAG: 0.46%
Aus	269	43.10%	55.80%	1.12%	0.00%	NA
Indica I	595	71.40%	25.90%	1.34%	0.00%	TGAGAGAG: 1.34%
Indica II	465	47.10%	42.20%	7.10%	1.29%	TGAGAGAG: 2.37%
Indica III	913	41.10%	37.80%	2.08%	8.76%	TGAGAGAG: 10.19%; A: 0.11%
Indica Intermediate	786	48.00%	37.30%	5.73%	0.64%	TGAGAGAG: 8.40%
Temperate Japonica	767	50.10%	37.50%	12.39%	0.00%	NA
Tropical Japonica	504	52.60%	38.50%	8.73%	0.00%	TGAGAGAG: 0.20%
Japonica Intermediate	241	48.10%	42.30%	7.05%	0.00%	TGAGAGAG: 2.49%
VI/Aromatic	96	37.50%	26.00%	19.79%	0.00%	A: 14.58%; AGGAGAGAG: 2.08%
Intermediate	90	45.60%	36.70%	13.33%	0.00%	TGAGAGAG: 3.33%; A: 1.11%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123942722	AGAGAGAG -> TGAGAGAG	LOC_Os11g40150.1	5_prime_UTR_premature_start_codon_gain_variant ; LOW	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> TGAGAGAG	LOC_Os11g40150.1	5_prime_UTR_variant ; 51.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> TGAGAGAG	LOC_Os11g40140.1	upstream_gene_variant ; 178.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> TGAGAGAG	LOC_Os11g40160.1	upstream_gene_variant ; 4318.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> A	LOC_Os11g40150.1	5_prime_UTR_variant ; 30.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> A	LOC_Os11g40140.1	upstream_gene_variant ; 179.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> A	LOC_Os11g40160.1	upstream_gene_variant ; 4317.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> AGGAGAGAG	LOC_Os11g40150.1	5_prime_UTR_variant ; 49.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> AGGAGAGAG	LOC_Os11g40140.1	upstream_gene_variant ; 180.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> AGGAGAGAG	LOC_Os11g40160.1	upstream_gene_variant ; 4316.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> DEL	N	N	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> GGAGAGAG	LOC_Os11g40150.1	5_prime_UTR_variant ; 51.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> GGAGAGAG	LOC_Os11g40140.1	upstream_gene_variant ; 178.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	N	N	N	N
vg1123942722	AGAGAGAG -> GGAGAGAG	LOC_Os11g40160.1	upstream_gene_variant ; 4318.0bp to feature; MODIFIER	silent_mutation	Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859	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)
vg1123942722	AGAGA*	A	-0.02	-0.03	-0.01	0.0	0.01	0.01
vg1123942722	AGAGA*	AGGAG*	0.09	0.11	0.1	0.04	0.06	0.07
vg1123942722	AGAGA*	GGAGA*	0.03	0.03	0.02	0.02	0.02	0.02
vg1123942722	AGAGA*	TGAGA*	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
vg1123942722	3.36E-06	3.35E-06	mr1396	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