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Detailed information for vg0335146664:

Variant ID: vg0335146664 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 35146664
Reference Allele: TTTTATAA	Alternative Allele: T
Primary Allele: TTTTATAA	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTTTTTTTGGGTGAATACTTGTGTTCATGATTAATTGTGCACGGATGCGTGCGTCTATGTACAGTTGCGTTTTACCTTCTCATTGACTTATTTTTCTG[TTTTATAA/T]
TTTGAATTAATTCTGCTTTATGTGTGTGTGTGTGTGTTTGCTGTCTGCTTTTCTTAATATTAAATTAATTTACAAGGTTTGGACTATGCATACATGCTAG

Reverse complement sequence

CTAGCATGTATGCATAGTCCAAACCTTGTAAATTAATTTAATATTAAGAAAAGCAGACAGCAAACACACACACACACACATAAAGCAGAATTAATTCAAA[TTATAAAA/A]
CAGAAAAATAAGTCAATGAGAAGGTAAAACGCAACTGTACATAGACGCACGCATCCGTGCACAATTAATCATGAACACAAGTATTCACCCAAAAAAAAGA

Allele Frequencies:

Populations	Population Size	Frequency of TTTTATAA(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.30%	16.20%	0.13%	0.34%	NA
All Indica	2759	72.40%	26.90%	0.18%	0.51%	NA
All Japonica	1512	99.60%	0.20%	0.07%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	82.20%	17.50%	0.00%	0.34%	NA
Indica II	465	44.70%	52.70%	0.86%	1.72%	NA
Indica III	913	84.20%	15.70%	0.00%	0.11%	NA
Indica Intermediate	786	67.60%	31.90%	0.13%	0.38%	NA
Temperate Japonica	767	99.60%	0.30%	0.00%	0.13%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	18.90%	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
vg0335146664	TTTTATAA -> T	LOC_Os03g62020.1	3_prime_UTR_variant ; 212.0bp to feature; MODIFIER	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	N	N	N	N
vg0335146664	TTTTATAA -> T	LOC_Os03g62040.1	upstream_gene_variant ; 3673.0bp to feature; MODIFIER	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	N	N	N	N
vg0335146664	TTTTATAA -> T	LOC_Os03g62030.1	downstream_gene_variant ; 576.0bp to feature; MODIFIER	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	N	N	N	N
vg0335146664	TTTTATAA -> T	LOC_Os03g62030.3	downstream_gene_variant ; 576.0bp to feature; MODIFIER	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	N	N	N	N
vg0335146664	TTTTATAA -> T	LOC_Os03g62030.4	downstream_gene_variant ; 576.0bp to feature; MODIFIER	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	N	N	N	N
vg0335146664	TTTTATAA -> T	LOC_Os03g62030.2	downstream_gene_variant ; 576.0bp to feature; MODIFIER	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	N	N	N	N
vg0335146664	TTTTATAA -> T	LOC_Os03g62030.5	downstream_gene_variant ; 576.0bp to feature; MODIFIER	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	N	N	N	N
vg0335146664	TTTTATAA -> T	LOC_Os03g62030.6	downstream_gene_variant ; 576.0bp to feature; MODIFIER	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	N	N	N	N
vg0335146664	TTTTATAA -> DEL	N	N	silent_mutation	Average:77.513; most accessible tissue: Zhenshan97 root, score: 89.064	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)
vg0335146664	TTTTA*	T	0.34	0.12	0.08	-0.05	-0.02	-0.08