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Detailed information for vg0427576932:

Variant ID: vg0427576932 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 27576932
Reference Allele: CTG	Alternative Allele: CTGTG,C,CTGTGTG
Primary Allele: CTGTG	Secondary Allele: CTG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGAGGAAGGTGGAGAAGAACTCGGCGAAGTACGCCCGGAGCGCCGGCGGCGAGAAGCAGCGCTTCATGTTGGCACAGATGTTCGCCATTGCAAGTTTACC[CTG/CTGTG,C,CTGTGTG]
TGTGTGTGTGTGACACTGTGTTTACAGAGCAGTGAAGAACACGATTACACGAATTCGCACAGTTCTTCACTACTCGGGGTGTCACAGACTTTATATAGAA

Reverse complement sequence

TTCTATATAAAGTCTGTGACACCCCGAGTAGTGAAGAACTGTGCGAATTCGTGTAATCGTGTTCTTCACTGCTCTGTAAACACAGTGTCACACACACACA[CAG/CACAG,G,CACACAG]
GGTAAACTTGCAATGGCGAACATCTGTGCCAACATGAAGCGCTGCTTCTCGCCGCCGGCGCTCCGGGCGTACTTCGCCGAGTTCTTCTCCACCTTCCTCT

Allele Frequencies:

Populations	Population Size	Frequency of CTGTG(primary allele)	Frequency of CTG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.90%	46.50%	0.13%	0.40%	CTGTGTG: 0.06%
All Indica	2759	82.30%	16.90%	0.18%	0.58%	CTGTGTG: 0.11%
All Japonica	1512	0.60%	99.30%	0.00%	0.13%	NA
Aus	269	70.30%	29.70%	0.00%	0.00%	NA
Indica I	595	78.20%	21.00%	0.34%	0.50%	NA
Indica II	465	91.20%	8.40%	0.00%	0.43%	NA
Indica III	913	82.40%	17.00%	0.11%	0.55%	NA
Indica Intermediate	786	80.00%	18.60%	0.25%	0.76%	CTGTGTG: 0.38%
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	0.60%	99.20%	0.00%	0.20%	NA
Japonica Intermediate	241	0.80%	98.80%	0.00%	0.41%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	35.60%	62.20%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0427576932	CTG -> C	LOC_Os04g46490.1	5_prime_UTR_variant ; 14.0bp to feature; MODIFIER	N	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> C	LOC_Os04g46480.1	upstream_gene_variant ; 4217.0bp to feature; MODIFIER	N	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> C	LOC_Os04g46480.2	upstream_gene_variant ; 4217.0bp to feature; MODIFIER	N	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> DEL	N	N	silent_mutation	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> CTGTG	LOC_Os04g46490.1	5_prime_UTR_variant ; 16.0bp to feature; MODIFIER	silent_mutation	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> CTGTG	LOC_Os04g46480.1	upstream_gene_variant ; 4219.0bp to feature; MODIFIER	silent_mutation	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> CTGTG	LOC_Os04g46480.2	upstream_gene_variant ; 4219.0bp to feature; MODIFIER	silent_mutation	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> CTGTGTG	LOC_Os04g46490.1	5_prime_UTR_variant ; 16.0bp to feature; MODIFIER	silent_mutation	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> CTGTGTG	LOC_Os04g46480.1	upstream_gene_variant ; 4219.0bp to feature; MODIFIER	silent_mutation	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	N	N	N	N
vg0427576932	CTG -> CTGTGTG	LOC_Os04g46480.2	upstream_gene_variant ; 4219.0bp to feature; MODIFIER	silent_mutation	Average:80.784; most accessible tissue: Zhenshan97 flower, score: 87.906	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)
vg0427576932	CTG	C	-0.2	-0.09	-0.11	-0.12	-0.21	-0.26
vg0427576932	CTG	CTGTG	0.09	0.14	0.09	0.08	0.07	0.04
vg0427576932	CTG	CTGTG*	0.26	0.17	0.11	0.14	0.21	0.22