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Detailed information for vg0700037240:

Variant ID: vg0700037240 (JBrowse)	Variation Type: INDEL
Chromosome: chr07	Position: 37240
Reference Allele: G	Alternative Allele: GTTCCTATCCAAGTGCATGTGGATCACTAGCTTATCACCTA,A
Primary Allele: GTTCCTATCCAAGTGCATGT GGATCACTAGCTTATCACCT A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTCTCCCCATACACACAAGAAAAAAAGAAACCACAAATTCATGTCATGAGAACTGTCAATTCATGTCATGAGAACTGTCAATTCATTGGTTTGATCAT[G/GTTCCTATCCAAGTGCATGTGGATCACTAGCTTATCACCTA,A]
TTAATTCTTGCATGTTTACCCTACTACTTCTCAAGTAGGCAGCACAAACTCTTCTGCTGAGGGATTATATAGCATGTTTGGCGCCTGTTGAGCATGTCCA

Reverse complement sequence

TGGACATGCTCAACAGGCGCCAAACATGCTATATAATCCCTCAGCAGAAGAGTTTGTGCTGCCTACTTGAGAAGTAGTAGGGTAAACATGCAAGAATTAA[C/TAGGTGATAAGCTAGTGATCCACATGCACTTGGATAGGAAC,T]
ATGATCAAACCAATGAATTGACAGTTCTCATGACATGAATTGACAGTTCTCATGACATGAATTTGTGGTTTCTTTTTTTCTTGTGTGTATGGGGAGAAAA

Allele Frequencies:

Populations	Population Size	Frequency of GTTCCTATCCAAGTGCATGT GGATCACTAGCTTATCACCT A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.80%	22.90%	0.11%	0.00%	A: 0.25%
All Indica	2759	94.30%	5.40%	0.07%	0.00%	A: 0.22%
All Japonica	1512	40.90%	58.70%	0.13%	0.00%	A: 0.26%
Aus	269	92.90%	6.70%	0.00%	0.00%	A: 0.37%
Indica I	595	90.60%	9.20%	0.17%	0.00%	NA
Indica II	465	93.50%	6.20%	0.00%	0.00%	A: 0.22%
Indica III	913	97.90%	1.80%	0.00%	0.00%	A: 0.33%
Indica Intermediate	786	93.30%	6.40%	0.13%	0.00%	A: 0.25%
Temperate Japonica	767	15.50%	84.40%	0.13%	0.00%	NA
Tropical Japonica	504	69.80%	29.40%	0.20%	0.00%	A: 0.60%
Japonica Intermediate	241	61.40%	38.20%	0.00%	0.00%	A: 0.41%
VI/Aromatic	96	96.90%	2.10%	0.00%	0.00%	A: 1.04%
Intermediate	90	73.30%	25.60%	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
vg0700037240	G -> GTTCCTATCCAAGTGCATGTGGATCACTAG CTTATCACCTA	LOC_Os07g01050.1	upstream_gene_variant ; 3505.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700037240	G -> GTTCCTATCCAAGTGCATGTGGATCACTAG CTTATCACCTA	LOC_Os07g01060.2	upstream_gene_variant ; 2656.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700037240	G -> GTTCCTATCCAAGTGCATGTGGATCACTAG CTTATCACCTA	LOC_Os07g01060.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700037240	G -> GTTCCTATCCAAGTGCATGTGGATCACTAG CTTATCACCTA	LOC_Os07g01060.3	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700037240	G -> A	LOC_Os07g01050.1	upstream_gene_variant ; 3504.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700037240	G -> A	LOC_Os07g01060.2	upstream_gene_variant ; 2657.0bp to feature; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700037240	G -> A	LOC_Os07g01060.1	intron_variant ; MODIFIER	silent_mutation	Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125	N	N	N	N
vg0700037240	G -> A	LOC_Os07g01060.3	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)
vg0700037240	G	A	0.0	-0.01	-0.01	-0.01	0.0	0.0
vg0700037240	G	GTTCC*	-0.04	-0.03	-0.05	-0.08	0.01	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0700037240	2.68E-06	6.64E-06	mr1209	Ind_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
vg0700037240	3.26E-06	5.04E-06	mr1217	Ind_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