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Detailed information for vg0823617230:

Variant ID: vg0823617230 (JBrowse)	Variation Type: INDEL
Chromosome: chr08	Position: 23617230
Reference Allele: GGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA	Alternative Allele: AGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA,G
Primary Allele: GGGAAATACGTACTCTATGG TGGGCATATCGTGCGTGTAG GAATTGA	Secondary Allele: AGGAAATACGTACTCTATGG TGGGCATATCGTGCGTGTAG GAATTGA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCCTATTTTGCTCCACGGAAAATATCCAGTCCTTTTTTACTCCACCGAAAATCGTCCTCTACTATTGCCGGTCTGCCAGTTGAAATTCGACCTCCCTAC[GGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA/AGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA,G]
TGAAATGCGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGATGCCATTTTGAACAACTATTCAGATTGATGGCATTTTGAACCATATTATTTTTA

Reverse complement sequence

TAAAAATAATATGGTTCAAAATGCCATCAATCTGAATAGTTGTTCAAAATGGCATCAATTCCTACACGCACGATATGCCCACCATAGAGTACGCATTTCA[TCAATTCCTACACGCACGATATGCCCACCATAGAGTACGTATTTCCC/TCAATTCCTACACGCACGATATGCCCACCATAGAGTACGTATTTCCT,C]
GTAGGGAGGTCGAATTTCAACTGGCAGACCGGCAATAGTAGAGGACGATTTTCGGTGGAGTAAAAAAGGACTGGATATTTTCCGTGGAGCAAAATAGGGC

Allele Frequencies:

Populations	Population Size	Frequency of GGGAAATACGTACTCTATGG TGGGCATATCGTGCGTGTAG GAATTGA(primary allele)	Frequency of AGGAAATACGTACTCTATGG TGGGCATATCGTGCGTGTAG GAATTGA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.20%	3.20%	0.61%	0.00%	G: 0.04%
All Indica	2759	99.80%	0.10%	0.04%	0.00%	G: 0.04%
All Japonica	1512	89.00%	9.30%	1.72%	0.00%	NA
Aus	269	99.30%	0.00%	0.37%	0.00%	G: 0.37%
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	99.60%	0.30%	0.00%	0.00%	G: 0.11%
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	99.60%	0.00%	0.39%	0.00%	NA
Tropical Japonica	504	70.60%	26.00%	3.37%	0.00%	NA
Japonica Intermediate	241	93.80%	3.70%	2.49%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	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
vg0823617230	GGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA -> G	LOC_Os08g37370.1	upstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:84.109; most accessible tissue: Minghui63 flag leaf, score: 98.339	N	N	N	N
vg0823617230	GGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA -> G	LOC_Os08g37370.2	upstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:84.109; most accessible tissue: Minghui63 flag leaf, score: 98.339	N	N	N	N
vg0823617230	GGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA -> G	LOC_Os08g37370-LOC_Os08g37380	intergenic_region ; MODIFIER	silent_mutation	Average:84.109; most accessible tissue: Minghui63 flag leaf, score: 98.339	N	N	N	N
vg0823617230	GGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA -> AGGAAATACGTACTCTATGGTGGGCATATC GTGCGTGTAGGAATTGA	LOC_Os08g37370.1	upstream_gene_variant ; 2523.0bp to feature; MODIFIER	silent_mutation	Average:84.109; most accessible tissue: Minghui63 flag leaf, score: 98.339	N	N	N	N
vg0823617230	GGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA -> AGGAAATACGTACTCTATGGTGGGCATATC GTGCGTGTAGGAATTGA	LOC_Os08g37370.2	upstream_gene_variant ; 2523.0bp to feature; MODIFIER	silent_mutation	Average:84.109; most accessible tissue: Minghui63 flag leaf, score: 98.339	N	N	N	N
vg0823617230	GGGAAATACGTACTCTATGGTGGGCATATCGTGCGTGTAGGAATTGA -> AGGAAATACGTACTCTATGGTGGGCATATC GTGCGTGTAGGAATTGA	LOC_Os08g37370-LOC_Os08g37380	intergenic_region ; MODIFIER	silent_mutation	Average:84.109; most accessible tissue: Minghui63 flag leaf, score: 98.339	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)
vg0823617230	GGGAA*	AGGAA*	-0.01	-0.06	-0.04	0.0	-0.02	-0.02
vg0823617230	GGGAA*	G	0.23	0.43	0.36	0.14	0.39	0.22

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0823617230	8.41E-07	8.41E-07	mr1448_2	Jap_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251