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Detailed information for vg0406950547:

Variant ID: vg0406950547 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 6950547
Reference Allele: ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG	Alternative Allele: GTGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG,A
Primary Allele: GTGTAGTTAAGTCACTGACA TGTGGGCCATAGCAAAGTAG GACCCACATGTCAGTGACTC AACTGCATG	Secondary Allele: ATGTAGTTAAGTCACTGACA TGTGGGCCATAGCAAAGTAG GACCCACATGTCAGTGACTC AACTGCATG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACACAAAGATCCTAATTTTAAGAGGTACTTTGATATTCCGAATTTTTTTTATGCATCCCCCCACCGTGCCGGGAAAGGGATCCTCTGACTTAACCGCC[ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG/GTGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG,A]
TGCAGTTAAGTCAGAGGATCTGCTCCCCCCCCCTCCCCAACCATTGAGGCTGTCTCTTGCATTTTCATTGCAGTGTAGAAAGTTTTGACACTAAAAACTC

Reverse complement sequence

GAGTTTTTAGTGTCAAAACTTTCTACACTGCAATGAAAATGCAAGAGACAGCCTCAATGGTTGGGGAGGGGGGGGGAGCAGATCCTCTGACTTAACTGCA[CATGCAGTTGAGTCACTGACATGTGGGTCCTACTTTGCTATGGCCCACATGTCAGTGACTTAACTACAT/CATGCAGTTGAGTCACTGACATGTGGGTCCTACTTTGCTATGGCCCACATGTCAGTGACTTAACTACAC,T]
GGCGGTTAAGTCAGAGGATCCCTTTCCCGGCACGGTGGGGGGATGCATAAAAAAAATTCGGAATATCAAAGTACCTCTTAAAATTAGGATCTTTGTGTGG

Allele Frequencies:

Populations	Population Size	Frequency of GTGTAGTTAAGTCACTGACA TGTGGGCCATAGCAAAGTAG GACCCACATGTCAGTGACTC AACTGCATG(primary allele)	Frequency of ATGTAGTTAAGTCACTGACA TGTGGGCCATAGCAAAGTAG GACCCACATGTCAGTGACTC AACTGCATG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.60%	46.00%	0.44%	1.99%	NA
All Indica	2759	75.50%	20.90%	0.51%	3.04%	NA
All Japonica	1512	1.10%	97.90%	0.46%	0.60%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	93.10%	6.20%	0.17%	0.50%	NA
Indica II	465	80.00%	18.30%	0.86%	0.86%	NA
Indica III	913	63.40%	29.70%	0.22%	6.68%	NA
Indica Intermediate	786	73.50%	23.50%	0.89%	2.04%	NA
Temperate Japonica	767	0.80%	97.40%	0.78%	1.04%	NA
Tropical Japonica	504	0.80%	99.00%	0.00%	0.20%	NA
Japonica Intermediate	241	2.50%	97.10%	0.41%	0.00%	NA
VI/Aromatic	96	43.80%	56.20%	0.00%	0.00%	NA
Intermediate	90	41.10%	57.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0406950547	ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG -> A	LOC_Os04g12550.1	downstream_gene_variant ; 793.0bp to feature; MODIFIER	N	Average:73.812; most accessible tissue: Zhenshan97 flower, score: 94.938	N	N	N	N
vg0406950547	ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG -> A	LOC_Os04g12560.1	downstream_gene_variant ; 4757.0bp to feature; MODIFIER	N	Average:73.812; most accessible tissue: Zhenshan97 flower, score: 94.938	N	N	N	N
vg0406950547	ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG -> A	LOC_Os04g12540-LOC_Os04g12550	intergenic_region ; MODIFIER	N	Average:73.812; most accessible tissue: Zhenshan97 flower, score: 94.938	N	N	N	N
vg0406950547	ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG -> DEL	N	N	silent_mutation	Average:73.812; most accessible tissue: Zhenshan97 flower, score: 94.938	N	N	N	N
vg0406950547	ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG -> GTGTAGTTAAGTCACTGACATGTGGGCCAT AGCAAAGTAGGACCCACATGTCAGTGACTC AACTGCATG	LOC_Os04g12550.1	downstream_gene_variant ; 794.0bp to feature; MODIFIER	silent_mutation	Average:73.812; most accessible tissue: Zhenshan97 flower, score: 94.938	N	N	N	N
vg0406950547	ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG -> GTGTAGTTAAGTCACTGACATGTGGGCCAT AGCAAAGTAGGACCCACATGTCAGTGACTC AACTGCATG	LOC_Os04g12560.1	downstream_gene_variant ; 4758.0bp to feature; MODIFIER	silent_mutation	Average:73.812; most accessible tissue: Zhenshan97 flower, score: 94.938	N	N	N	N
vg0406950547	ATGTAGTTAAGTCACTGACATGTGGGCCATAGCAAAGTAGGACCCACATGTCAGTGACTCAACTGCATG -> GTGTAGTTAAGTCACTGACATGTGGGCCAT AGCAAAGTAGGACCCACATGTCAGTGACTC AACTGCATG	LOC_Os04g12540-LOC_Os04g12550	intergenic_region ; MODIFIER	silent_mutation	Average:73.812; most accessible tissue: Zhenshan97 flower, score: 94.938	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)
vg0406950547	ATGTA*	A	-0.23	-0.3	-0.1	-0.35	-0.19	-0.19
vg0406950547	ATGTA*	GTGTA*	0.0	0.02	0.02	0.01	-0.01	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406950547	NA	7.53E-06	mr1166	Ind_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
vg0406950547	NA	3.55E-06	mr1515	Ind_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
vg0406950547	NA	5.66E-06	mr1537	Ind_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
vg0406950547	NA	1.00E-06	mr1649	Ind_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
vg0406950547	1.91E-06	NA	mr1891	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