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Detailed information for vg0500579714:

Variant ID: vg0500579714 (JBrowse)	Variation Type: INDEL
Chromosome: chr05	Position: 579714
Reference Allele: C	Alternative Allele: CTAAGAACACAAGTTGATAGTG,CTAAGAACACAAGTTGATTGTG
Primary Allele: CTAAGAACACAAGTTGATAG TG	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACAGAGATATGACTGATTGATTGGATACTTCAGAAATTTTTTTTAAAAAAAAAACTAAAGGAAAAAAAAAGGAATAAACATAGCATACATGTCTAGATT[C/CTAAGAACACAAGTTGATAGTG,CTAAGAACACAAGTTGATTGTG]
TAATCACCATAGTAAGAAATGCTATATGGAGGAAGGAAGAAGAGAGGAGAAAGGTGAGACGCACCAGAAGGGGAGGAGGCGCTGCGGCAAGGGCTCTCCG

Reverse complement sequence

CGGAGAGCCCTTGCCGCAGCGCCTCCTCCCCTTCTGGTGCGTCTCACCTTTCTCCTCTCTTCTTCCTTCCTCCATATAGCATTTCTTACTATGGTGATTA[G/CACTATCAACTTGTGTTCTTAG,CACAATCAACTTGTGTTCTTAG]
AATCTAGACATGTATGCTATGTTTATTCCTTTTTTTTTCCTTTAGTTTTTTTTTTAAAAAAAATTTCTGAAGTATCCAATCAATCAGTCATATCTCTGTG

Allele Frequencies:

Populations	Population Size	Frequency of CTAAGAACACAAGTTGATAG TG(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.40%	19.60%	0.00%	0.00%	CTAAGAACACAAGTTGATTGTG: 0.02%
All Indica	2759	98.70%	1.30%	0.00%	0.00%	CTAAGAACACAAGTTGATTGTG: 0.04%
All Japonica	1512	43.50%	56.50%	0.00%	0.00%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	98.30%	1.50%	0.00%	0.00%	CTAAGAACACAAGTTGATTGTG: 0.17%
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.70%	1.30%	0.00%	0.00%	NA
Temperate Japonica	767	17.90%	82.10%	0.00%	0.00%	NA
Tropical Japonica	504	72.20%	27.80%	0.00%	0.00%	NA
Japonica Intermediate	241	64.70%	35.30%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	73.30%	26.70%	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
vg0500579714	C -> CTAAGAACACAAGTTGATAGTG	LOC_Os05g02010.1	downstream_gene_variant ; 2849.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATAGTG	LOC_Os05g02010.2	downstream_gene_variant ; 2849.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATAGTG	LOC_Os05g02010.3	downstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATAGTG	LOC_Os05g02010.4	downstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATAGTG	LOC_Os05g02020.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATAGTG	LOC_Os05g02020.2	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATTGTG	LOC_Os05g02010.1	downstream_gene_variant ; 2849.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATTGTG	LOC_Os05g02010.2	downstream_gene_variant ; 2849.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATTGTG	LOC_Os05g02010.3	downstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATTGTG	LOC_Os05g02010.4	downstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATTGTG	LOC_Os05g02020.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0500579714	C -> CTAAGAACACAAGTTGATTGTG	LOC_Os05g02020.2	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	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)
vg0500579714	C	CTAAG*	-0.05	-0.04	-0.1	-0.14	-0.13	-0.09