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Detailed information for vg0205347357:

Variant ID: vg0205347357 (JBrowse)	Variation Type: INDEL
Chromosome: chr02	Position: 5347357
Reference Allele: CGGCGGCGGAGGCCGA	Alternative Allele: CGGCGGCGGAGGCCGAGGCGGCGGAGGCCGA,C
Primary Allele: CGGCGGCGGAGGCCGA	Secondary Allele: CGGCGGCGGAGGCCGAGGCG GCGGAGGCCGA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAAAGAAGCCCACAGATCAAACGGGTCACCCACAAACTCAAGGGGGGGGGTGGAATCAGGCAGGGGGAGCAAGAGGGCAAACCCTAACCCTGGTCGCGG[CGGCGGCGGAGGCCGA/CGGCGGCGGAGGCCGAGGCGGCGGAGGCCGA,C]
GGCGGCGGTGGCGGAGGAGGCGTGCGGGGATTGGAATCGCGAGCTCGGTGCGCGTGGTGGCGTCTCCTCTCTCTCTCTCTCTCTCTCTCTCACTCTCTCT

Reverse complement sequence

AGAGAGAGTGAGAGAGAGAGAGAGAGAGAGAGAGGAGACGCCACCACGCGCACCGAGCTCGCGATTCCAATCCCCGCACGCCTCCTCCGCCACCGCCGCC[TCGGCCTCCGCCGCCG/TCGGCCTCCGCCGCCTCGGCCTCCGCCGCCG,G]
CCGCGACCAGGGTTAGGGTTTGCCCTCTTGCTCCCCCTGCCTGATTCCACCCCCCCCCTTGAGTTTGTGGGTGACCCGTTTGATCTGTGGGCTTCTTTTT

Allele Frequencies:

Populations	Population Size	Frequency of CGGCGGCGGAGGCCGA(primary allele)	Frequency of CGGCGGCGGAGGCCGAGGCG GCGGAGGCCGA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.90%	0.10%	0.00%	0.00%	C: 0.02%
All Indica	2759	99.80%	0.20%	0.00%	0.00%	C: 0.04%
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.50%	0.40%	0.00%	0.00%	C: 0.11%
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0205347357	CGGCGGCGGAGGCCGA -> CGGCGGCGGAGGCCGAGGCGGCGGAGGCCG A	LOC_Os02g10200.1	5_prime_UTR_variant ; 815.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> CGGCGGCGGAGGCCGAGGCGGCGGAGGCCG A	LOC_Os02g10200.2	5_prime_UTR_variant ; 815.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> CGGCGGCGGAGGCCGAGGCGGCGGAGGCCG A	LOC_Os02g10210.1	upstream_gene_variant ; 1347.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> CGGCGGCGGAGGCCGAGGCGGCGGAGGCCG A	LOC_Os02g10220.1	upstream_gene_variant ; 4094.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> CGGCGGCGGAGGCCGAGGCGGCGGAGGCCG A	LOC_Os02g10190.1	downstream_gene_variant ; 2855.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> C	LOC_Os02g10200.1	5_prime_UTR_variant ; 800.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> C	LOC_Os02g10200.2	5_prime_UTR_variant ; 800.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> C	LOC_Os02g10210.1	upstream_gene_variant ; 1362.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> C	LOC_Os02g10220.1	upstream_gene_variant ; 4109.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	N	N	N	N
vg0205347357	CGGCGGCGGAGGCCGA -> C	LOC_Os02g10190.1	downstream_gene_variant ; 2840.0bp to feature; MODIFIER	N	Average:98.228; most accessible tissue: Zhenshan97 flower, score: 99.344	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)
vg0205347357	CGGCG*	C	-0.02	-0.06	-0.06	-0.08	-0.05	-0.07
vg0205347357	CGGCG*	CGGCG*	0.02	0.1	0.17	0.03	0.07	0.09