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Detailed information for vg1105978986:

Variant ID: vg1105978986 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 5978986
Reference Allele: G	Alternative Allele: GACTACGAGCTAATTAATATGGCTGTGCATCCACTA,GA,GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA
Primary Allele: G	Secondary Allele: GA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCGGTTCCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGTGGCATCGTCGAGATCGACCTCTACCTGAAGCACTA[G/GACTACGAGCTAATTAATATGGCTGTGCATCCACTA,GA,GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA]
CTAGAAGTAGCACGGAGCTAGCCATGGACAGAAAACGCACGCGACCACTGCATATATGCATGTCTGGCCGCTGCATCGTCTGTGCGACGAGTTGTGCAGC

Reverse complement sequence

GCTGCACAACTCGTCGCACAGACGATGCAGCGGCCAGACATGCATATATGCAGTGGTCGCGTGCGTTTTCTGTCCATGGCTAGCTCCGTGCTACTTCTAG[C/TAGTGGATGCACAGCCATATTAATTAGCTCGTAGTC,TC,TTTTGTAGTAGTGGATGCACAGCCATATTAATTAGCTCGTAGTC]
TAGTGCTTCAGGTAGAGGTCGATCTCGACGATGCCACCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGGAACCGCC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of GA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	69.30%	0.10%	14.07%	16.53%	GACTACGAGCTAATTAATATGGCTGTGCATCCACTA: 0.04%; GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA: 0.02%
All Indica	2759	57.80%	0.10%	19.10%	22.91%	GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA: 0.04%; GACTACGAGCTAATTAATATGGCTGTGCATCCACTA: 0.04%
All Japonica	1512	93.10%	0.00%	1.26%	5.69%	NA
Aus	269	43.10%	0.40%	40.15%	15.99%	GACTACGAGCTAATTAATATGGCTGTGCATCCACTA: 0.37%
Indica I	595	56.50%	0.00%	18.32%	25.21%	NA
Indica II	465	42.80%	0.20%	21.94%	35.05%	NA
Indica III	913	66.40%	0.00%	19.61%	13.91%	GACTACGAGCTAATTAATATGGCTGTGCATCCACTACTACAAAA: 0.11%
Indica Intermediate	786	57.80%	0.30%	17.43%	24.43%	GACTACGAGCTAATTAATATGGCTGTGCATCCACTA: 0.13%
Temperate Japonica	767	88.80%	0.00%	1.83%	9.39%	NA
Tropical Japonica	504	97.80%	0.00%	0.60%	1.59%	NA
Japonica Intermediate	241	96.70%	0.00%	0.83%	2.49%	NA
VI/Aromatic	96	89.60%	0.00%	5.21%	5.21%	NA
Intermediate	90	76.70%	0.00%	6.67%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105978986	G -> GA	LOC_Os11g10860.1	upstream_gene_variant ; 1777.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GA	LOC_Os11g10840.1	downstream_gene_variant ; 4464.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GA	LOC_Os11g10850.1	downstream_gene_variant ; 1.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GA	LOC_Os11g10850-LOC_Os11g10860	intergenic_region ; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GACTACGAGCTAATTAATATGGCTGTGCAT CCACTA	LOC_Os11g10860.1	upstream_gene_variant ; 1777.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GACTACGAGCTAATTAATATGGCTGTGCAT CCACTA	LOC_Os11g10840.1	downstream_gene_variant ; 4464.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GACTACGAGCTAATTAATATGGCTGTGCAT CCACTA	LOC_Os11g10850.1	downstream_gene_variant ; 1.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GACTACGAGCTAATTAATATGGCTGTGCAT CCACTA	LOC_Os11g10850-LOC_Os11g10860	intergenic_region ; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> DEL	LOC_Os11g10850.1	N	frameshift_variant	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GACTACGAGCTAATTAATATGGCTGTGCAT CCACTACTACAAAA	LOC_Os11g10860.1	upstream_gene_variant ; 1777.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GACTACGAGCTAATTAATATGGCTGTGCAT CCACTACTACAAAA	LOC_Os11g10840.1	downstream_gene_variant ; 4464.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GACTACGAGCTAATTAATATGGCTGTGCAT CCACTACTACAAAA	LOC_Os11g10850.1	downstream_gene_variant ; 1.0bp to feature; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	N	N	N	N
vg1105978986	G -> GACTACGAGCTAATTAATATGGCTGTGCAT CCACTACTACAAAA	LOC_Os11g10850-LOC_Os11g10860	intergenic_region ; MODIFIER	silent_mutation	Average:89.764; most accessible tissue: Zhenshan97 flag leaf, score: 95.367	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)
vg1105978986	G	GA	0.05	0.02	0.0	-0.03	0.03	0.03
vg1105978986	G	GACTA*	0.0	-0.01	-0.02	-0.27	-0.18	-0.09