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Detailed information for vg0207063677:

Variant ID: vg0207063677 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 7063677
Reference Allele: AAGCAGCAGCAGCAGC	Alternative Allele: AAGCAGCAGCAGCAGCAGC,A,AAGCAGCAGCAGCAGCAGCAGC,AAGCAGCAGC
Primary Allele: AAGCAGCAGCAGCAGC	Secondary Allele: AAGCAGCAGCAGCAGCAGC

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTCCTCGCGCTCGACGCCGCGTACCCGCTGCCCCTCCTCCCCGGCATGCTCGAGAAGTTCCCCAAGACCGTCGAGCCGACCCGGTGGTGGCCGAAGAAG[AAGCAGCAGCAGCAGC/AAGCAGCAGCAGCAGCAGC,A,AAGCAGCAGCAGCAGCAGCAGC,AAGCAGCAGC]
AGCAGCAGCGCGCTGCGGTGAACAAGTCGAACAGCTTCGGCAGCAGCAGCCGCCGCCGCGGCGCACGCGGCAACGGCTGGACGCCGGAGCTGGAGGAGGA

Reverse complement sequence

TCCTCCTCCAGCTCCGGCGTCCAGCCGTTGCCGCGTGCGCCGCGGCGGCGGCTGCTGCTGCCGAAGCTGTTCGACTTGTTCACCGCAGCGCGCTGCTGCT[GCTGCTGCTGCTGCTT/GCTGCTGCTGCTGCTGCTT,T,GCTGCTGCTGCTGCTGCTGCTT,GCTGCTGCTT]
CTTCTTCGGCCACCACCGGGTCGGCTCGACGGTCTTGGGGAACTTCTCGAGCATGCCGGGGAGGAGGGGCAGCGGGTACGCGGCGTCGAGCGCGAGGACC

Allele Frequencies:

Populations	Population Size	Frequency of AAGCAGCAGCAGCAGC(primary allele)	Frequency of AAGCAGCAGCAGCAGCAGC(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.50%	32.20%	0.74%	0.00%	A: 4.23%; AAGCAGCAGCAGCAGCAGCAGC: 0.19%; AAGCAGCAGC: 0.04%
All Indica	2759	72.80%	22.80%	0.47%	0.00%	A: 3.91%
All Japonica	1512	42.20%	55.60%	1.26%	0.00%	AAGCAGCAGCAGCAGCAGCAGC: 0.60%; A: 0.26%; AAGCAGCAGC: 0.07%
Aus	269	66.90%	2.20%	0.00%	0.00%	A: 30.86%
Indica I	595	59.80%	27.70%	0.00%	0.00%	A: 12.44%
Indica II	465	87.70%	11.20%	1.08%	0.00%	NA
Indica III	913	73.80%	25.30%	0.33%	0.00%	A: 0.55%
Indica Intermediate	786	72.60%	23.00%	0.64%	0.00%	A: 3.69%
Temperate Japonica	767	69.00%	28.70%	1.69%	0.00%	A: 0.52%; AAGCAGCAGCAGCAGCAGCAGC: 0.13%
Tropical Japonica	504	11.50%	87.50%	0.40%	0.00%	AAGCAGCAGCAGCAGCAGCAGC: 0.40%; AAGCAGCAGC: 0.20%
Japonica Intermediate	241	21.20%	74.70%	1.66%	0.00%	AAGCAGCAGCAGCAGCAGCAGC: 2.49%
VI/Aromatic	96	74.00%	24.00%	1.04%	0.00%	AAGCAGCAGC: 1.04%
Intermediate	90	64.40%	27.80%	2.22%	0.00%	A: 5.56%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0207063677	AAGCAGCAGCAGCAGC -> AAGCAGCAGCAGCAGCAGC	LOC_Os02g13260.1	disruptive_inframe_insertion ; p.Gln246dup; MODERATE	inframe_variant	Average:84.844; most accessible tissue: Zhenshan97 flower, score: 92.936	N	N	N	N
vg0207063677	AAGCAGCAGCAGCAGC -> AAGCAGCAGCAGCAGCAGCAGC	LOC_Os02g13260.1	disruptive_inframe_insertion ; p.Gln245_Gln246dup; MODERATE	inframe_variant	Average:84.844; most accessible tissue: Zhenshan97 flower, score: 92.936	N	N	N	N
vg0207063677	AAGCAGCAGCAGCAGC -> AAGCAGCAGC	LOC_Os02g13260.1	disruptive_inframe_deletion ; p.Gln245_Gln246del; MODERATE	inframe_variant	Average:84.844; most accessible tissue: Zhenshan97 flower, score: 92.936	N	N	N	N
vg0207063677	AAGCAGCAGCAGCAGC -> A	LOC_Os02g13260.1	disruptive_inframe_deletion ; p.Gln242_Gln246del; MODERATE	inframe_variant	Average:84.844; most accessible tissue: Zhenshan97 flower, score: 92.936	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)
vg0207063677	AAGCA*	A	-0.04	-0.33	-0.42	-0.04	-0.14	-0.13
vg0207063677	AAGCA*	AAGCA*	0.1	-0.1	-0.15	0.0	0.01	-0.02