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Detailed information for vg0729587167:

Variant ID: vg0729587167 (JBrowse)	Variation Type: INDEL
Chromosome: chr07	Position: 29587167
Reference Allele: GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA	Alternative Allele: ATGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA,G
Primary Allele: ATGTAAGTCATTCTAGCATT TTCCACATTCATATTGATGT TAATGATCCGTTTCACAA	Secondary Allele: GTGTAAGTCATTCTAGCATT TTCCACATTCATATTGATGT TAATGATCCGTTTCACAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCCTACTTGACGACAACTAGTACTTTTTTTGCGGGGAGACGGCGACTAGTATTGTACTCCTTTTTTCATTACATAATCGTATACTCCCTCCGTTTCACA[GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA/ATGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA,G]
TGTAAGTCATTCTAGCATTTCCCACATTCATATTGATGTTAATGAATCTAGACATAACATCAATATAAATGTGAAAAATGCTAAAATGACTTATATTTGT

Reverse complement sequence

ACAAATATAAGTCATTTTAGCATTTTTCACATTTATATTGATGTTATGTCTAGATTCATTAACATCAATATGAATGTGGGAAATGCTAGAATGACTTACA[TTGTGAAACGGATCATTAACATCAATATGAATGTGGAAAATGCTAGAATGACTTACAC/TTGTGAAACGGATCATTAACATCAATATGAATGTGGAAAATGCTAGAATGACTTACAT,C]
TGTGAAACGGAGGGAGTATACGATTATGTAATGAAAAAAGGAGTACAATACTAGTCGCCGTCTCCCCGCAAAAAAAGTACTAGTTGTCGTCAAGTAGGGG

Allele Frequencies:

Populations	Population Size	Frequency of ATGTAAGTCATTCTAGCATT TTCCACATTCATATTGATGT TAATGATCCGTTTCACAA(primary allele)	Frequency of GTGTAAGTCATTCTAGCATT TTCCACATTCATATTGATGT TAATGATCCGTTTCACAA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.70%	25.30%	2.22%	0.00%	G: 6.77%
All Indica	2759	90.20%	6.10%	3.12%	0.00%	G: 0.58%
All Japonica	1512	16.70%	62.70%	1.06%	0.00%	G: 19.51%
Aus	269	84.40%	14.50%	0.74%	0.00%	G: 0.37%
Indica I	595	95.80%	1.20%	2.02%	0.00%	G: 1.01%
Indica II	465	92.90%	4.90%	2.15%	0.00%	NA
Indica III	913	88.50%	9.90%	1.42%	0.00%	G: 0.22%
Indica Intermediate	786	86.30%	6.20%	6.49%	0.00%	G: 1.02%
Temperate Japonica	767	0.90%	93.90%	0.00%	0.00%	G: 5.22%
Tropical Japonica	504	32.70%	19.00%	2.98%	0.00%	G: 45.24%
Japonica Intermediate	241	33.60%	54.80%	0.41%	0.00%	G: 11.20%
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	57.80%	32.20%	1.11%	0.00%	G: 8.89%

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49390.1	upstream_gene_variant ; 4018.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49400.1	upstream_gene_variant ; 816.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49400.3	upstream_gene_variant ; 816.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49400.4	upstream_gene_variant ; 816.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49400.2	upstream_gene_variant ; 671.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49410.1	downstream_gene_variant ; 2727.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49410.2	downstream_gene_variant ; 2588.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49410.3	downstream_gene_variant ; 2727.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> G	LOC_Os07g49400-LOC_Os07g49410	intergenic_region ; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49390.1	upstream_gene_variant ; 4017.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49400.1	upstream_gene_variant ; 815.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49400.3	upstream_gene_variant ; 815.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49400.4	upstream_gene_variant ; 815.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49400.2	upstream_gene_variant ; 670.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49410.1	downstream_gene_variant ; 2728.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49410.2	downstream_gene_variant ; 2589.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49410.3	downstream_gene_variant ; 2728.0bp to feature; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	N	N	N	N
vg0729587167	GTGTAAGTCATTCTAGCATTTTCCACATTCATATTGATGTTAATGATCCGTTTCACAA -> ATGTAAGTCATTCTAGCATTTTCCACATTC ATATTGATGTTAATGATCCGTTTCACAA	LOC_Os07g49400-LOC_Os07g49410	intergenic_region ; MODIFIER	silent_mutation	Average:92.32; most accessible tissue: Zhenshan97 root, score: 98.012	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)
vg0729587167	GTGTA*	ATGTA*	-0.03	0.04	0.0	-0.05	-0.04	-0.03
vg0729587167	GTGTA*	G	0.03	0.49	0.72	0.43	0.4	0.44

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0729587167	NA	7.73E-06	mr1039	Jap_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
vg0729587167	NA	7.70E-06	mr1133	Jap_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
vg0729587167	NA	8.74E-36	mr1448	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
vg0729587167	NA	1.05E-30	mr1638	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
vg0729587167	NA	3.96E-21	mr1689	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
vg0729587167	NA	2.75E-07	mr1696	Jap_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
vg0729587167	NA	4.41E-06	mr1837	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
vg0729587167	NA	2.89E-24	mr1862	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
vg0729587167	NA	9.49E-10	mr1945	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