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Detailed information for vg0427576394:

Variant ID: vg0427576394 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 27576394
Reference Allele: T	Alternative Allele: TGTG
Primary Allele: TGTG	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAACGTGAGCACCCCCTCCAGGATCCCCGCCCCGAACCCGGTCATCTCCACCGCGATCCTCGTCGTCGGCACGGCCTGTGTGTGCAAACGCGCGTTAGTC[T/TGTG]
ACGCAAAGTTAAGGACATTTCGATCGGAAGTGATCTTGCCTGGCCGGCGGAGATGTAGTGGAGGACGAGGCAGGCGAACGTGGAGCCGAGCATCTGAGAC

Reverse complement sequence

GTCTCAGATGCTCGGCTCCACGTTCGCCTGCCTCGTCCTCCACTACATCTCCGCCGGCCAGGCAAGATCACTTCCGATCGAAATGTCCTTAACTTTGCGT[A/CACA]
GACTAACGCGCGTTTGCACACACAGGCCGTGCCGACGACGAGGATCGCGGTGGAGATGACCGGGTTCGGGGCGGGGATCCTGGAGGGGGTGCTCACGTTC

Allele Frequencies:

Populations	Population Size	Frequency of TGTG(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.00%	45.60%	0.21%	0.23%	NA
All Indica	2759	83.80%	15.50%	0.25%	0.40%	NA
All Japonica	1512	0.60%	99.30%	0.13%	0.00%	NA
Aus	269	72.90%	27.10%	0.00%	0.00%	NA
Indica I	595	80.30%	19.00%	0.17%	0.50%	NA
Indica II	465	92.30%	7.10%	0.22%	0.43%	NA
Indica III	913	83.10%	16.30%	0.33%	0.22%	NA
Indica Intermediate	786	82.30%	16.90%	0.25%	0.51%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	0.60%	99.20%	0.20%	0.00%	NA
Japonica Intermediate	241	0.80%	98.80%	0.41%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	35.60%	63.30%	1.11%	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
vg0427576394	T -> DEL	N	N	silent_mutation	Average:85.058; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0427576394	T -> TGTG	LOC_Os04g46480.1	upstream_gene_variant ; 3679.0bp to feature; MODIFIER	silent_mutation	Average:85.058; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0427576394	T -> TGTG	LOC_Os04g46480.2	upstream_gene_variant ; 3679.0bp to feature; MODIFIER	silent_mutation	Average:85.058; most accessible tissue: Zhenshan97 panicle, score: 93.657	N	N	N	N
vg0427576394	T -> TGTG	LOC_Os04g46490.1	intron_variant ; MODIFIER	silent_mutation	Average:85.058; most accessible tissue: Zhenshan97 panicle, score: 93.657	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)
vg0427576394	T	TGTG	-0.07	-0.09	-0.12	-0.14	-0.13	-0.14