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Detailed information for vg0305993129:

Variant ID: vg0305993129 (JBrowse)	Variation Type: INDEL
Chromosome: chr03	Position: 5993129
Reference Allele: TTTATGTTTTTGTGAG	Alternative Allele: CTTATGTTTTTGTGAG,TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG,T,TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG,TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG,TTTTAGTCCCTTCTATAGAGACTTATGTTTTTGTGAG
Primary Allele: CTTATGTTTTTGTGAG	Secondary Allele: TTTATGTTTTTGTGAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGGTTCAAATCAGAGCCAAACTAATCAGTAGCATAGTACAAGCAAATAATGATGTTACGGTGGTGTTTGGGAAGGAGGGATTAGTCCCTCTCATAGGAA[TTTATGTTTTTGTGAG/CTTATGTTTTTGTGAG,TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG,T,TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG,TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG,TTTTAGTCCCTTCTATAGAGACTTATGTTTTTGTGAG]
TTTAGTCCCTGCTTTTCAAACATCACCTATATTGTTCTCAAGTTGAATGTGCTGTGTTGTCTTGTTCCAATAGCATTCTTCTGCGTATATATAAACTTTG

Reverse complement sequence

CAAAGTTTATATATACGCAGAAGAATGCTATTGGAACAAGACAACACAGCACATTCAACTTGAGAACAATATAGGTGATGTTTGAAAAGCAGGGACTAAA[CTCACAAAAACATAAA/CTCACAAAAACATAAG,CTCACAAAAACATAAGTCCTTATAGGAGGGACTAAAA,A,CTCACAAAAACATAAGTCTCTATAGGAGGGACTAAAA,CTCACAAAAACATAAGTCTCTATAGGAGGGATTAAAA,CTCACAAAAACATAAGTCTCTATAGAAGGGACTAAAA]
TTCCTATGAGAGGGACTAATCCCTCCTTCCCAAACACCACCGTAACATCATTATTTGCTTGTACTATGCTACTGATTAGTTTGGCTCTGATTTGAACCTG

Allele Frequencies:

Populations	Population Size	Frequency of CTTATGTTTTTGTGAG(primary allele)	Frequency of TTTATGTTTTTGTGAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.10%	34.60%	0.70%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 23.61%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 2.26%; TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.97%; T: 0.68%; TTTTAGTCCCTTCTATAGAGACTTATGTTTTTGTGAG: 0.06%
All Indica	2759	51.80%	2.60%	0.98%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 39.58%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 3.62%; T: 1.09%; TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.29%
All Japonica	1512	0.30%	98.70%	0.07%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 0.40%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.33%; TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.07%; TTTTAGTCCCTTCTATAGAGACTTATGTTTTTGTGAG: 0.07%
Aus	269	80.30%	6.70%	1.12%	0.00%	TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 11.52%; T: 0.37%
Indica I	595	37.10%	1.30%	1.68%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 53.45%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 5.21%; T: 1.18%
Indica II	465	38.10%	4.70%	0.86%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 52.04%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 3.23%; T: 0.86%; TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.22%
Indica III	913	70.40%	2.00%	0.33%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 25.63%; T: 0.88%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.66%; TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.11%
Indica Intermediate	786	49.40%	3.20%	1.27%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 37.91%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 6.11%; T: 1.40%; TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.76%
Temperate Japonica	767	0.40%	98.00%	0.13%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 0.65%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.65%; TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 0.13%
Tropical Japonica	504	0.20%	99.60%	0.00%	0.00%	TTTTAGTCCCTTCTATAGAGACTTATGTTTTTGTGAG: 0.20%
Japonica Intermediate	241	0.40%	99.20%	0.00%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 0.41%
VI/Aromatic	96	81.20%	10.40%	1.04%	0.00%	TTTTAATCCCTCCTATAGAGACTTATGTTTTTGTGAG: 6.25%; T: 1.04%
Intermediate	90	30.00%	44.40%	1.11%	0.00%	TTTTAGTCCCTCCTATAAGGACTTATGTTTTTGTGAG: 20.00%; TTTTAGTCCCTCCTATAGAGACTTATGTTTTTGTGAG: 2.22%; TTTTAGTCCCTTCTATAGAGACTTATGTTTTTGTGAG: 2.22%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0305993129	TTTATGTTTTTGTGAG -> T	LOC_Os03g11550.1	upstream_gene_variant ; 4302.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> T	LOC_Os03g11550.2	upstream_gene_variant ; 4302.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> T	LOC_Os03g11560.1	downstream_gene_variant ; 1000.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> T	LOC_Os03g11550-LOC_Os03g11560	intergenic_region ; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTCCTATAAGGACTTATGTTT TTGTGAG	LOC_Os03g11550.1	upstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTCCTATAAGGACTTATGTTT TTGTGAG	LOC_Os03g11550.2	upstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTCCTATAAGGACTTATGTTT TTGTGAG	LOC_Os03g11560.1	downstream_gene_variant ; 998.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTCCTATAAGGACTTATGTTT TTGTGAG	LOC_Os03g11550-LOC_Os03g11560	intergenic_region ; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTTCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550.1	upstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTTCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550.2	upstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTTCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11560.1	downstream_gene_variant ; 998.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTTCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550-LOC_Os03g11560	intergenic_region ; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> CTTATGTTTTTGTGAG	LOC_Os03g11550.1	upstream_gene_variant ; 4301.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> CTTATGTTTTTGTGAG	LOC_Os03g11550.2	upstream_gene_variant ; 4301.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> CTTATGTTTTTGTGAG	LOC_Os03g11560.1	downstream_gene_variant ; 1001.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> CTTATGTTTTTGTGAG	LOC_Os03g11550-LOC_Os03g11560	intergenic_region ; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTCCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550.1	upstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTCCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550.2	upstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTCCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11560.1	downstream_gene_variant ; 998.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAGTCCCTCCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550-LOC_Os03g11560	intergenic_region ; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAATCCCTCCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550.1	upstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAATCCCTCCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550.2	upstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAATCCCTCCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11560.1	downstream_gene_variant ; 998.0bp to feature; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	N	N	N	N
vg0305993129	TTTATGTTTTTGTGAG -> TTTTAATCCCTCCTATAGAGACTTATGTTT TTGTGAG	LOC_Os03g11550-LOC_Os03g11560	intergenic_region ; MODIFIER	silent_mutation	Average:82.003; most accessible tissue: Zhenshan97 flower, score: 92.38	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)
vg0305993129	TTTAT*	CTTAT*	-0.07	-0.07	-0.03	0.0	-0.03	-0.02
vg0305993129	TTTAT*	T	-0.29	-0.26	-0.04	0.15	-0.03	-0.13
vg0305993129	TTTAT*	TTTTA*	-0.38	-0.31	-0.1	0.05	-0.09	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0305993129	NA	1.96E-06	mr1028	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
vg0305993129	NA	2.45E-07	mr1369	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0305993129	NA	2.75E-07	mr1453	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251