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Detailed information for vg0719701370:

Variant ID: vg0719701370 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19701370
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATAGATGGCCATATGGCCCGAGGCCCACGGCCCGGCCTGAAGCACACTATTTTGGCCCGGCCCAAGCATGGCACGGCCTGACTAGGGTCATGCCCGTAC[C/T]
GGCCCGGCTCGACAGCCGGGTCGTGCCTGGGCTGCACCCTCGGCACGGTGGACCGGCCCGGCACGGCCCGATCAAATAAAAAAATATTGGGATGCAAAAT

Reverse complement sequence

ATTTTGCATCCCAATATTTTTTTATTTGATCGGGCCGTGCCGGGCCGGTCCACCGTGCCGAGGGTGCAGCCCAGGCACGACCCGGCTGTCGAGCCGGGCC[G/A]
GTACGGGCATGACCCTAGTCAGGCCGTGCCATGCTTGGGCCGGGCCAAAATAGTGTGCTTCAGGCCGGGCCGTGGGCCTCGGGCCATATGGCCATCTATA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	83.50%	6.00%	0.28%	10.22%	NA
All Indica	2759	98.40%	1.50%	0.00%	0.14%	NA
All Japonica	1512	67.40%	0.40%	0.86%	31.35%	NA
Aus	269	13.80%	86.20%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	95.80%	3.70%	0.00%	0.51%	NA
Temperate Japonica	767	58.40%	0.50%	1.17%	39.90%	NA
Tropical Japonica	504	67.30%	0.00%	0.79%	31.94%	NA
Japonica Intermediate	241	96.30%	0.80%	0.00%	2.90%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	92.20%	2.20%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0719701370	C -> DEL	N	N	silent_mutation	Average:80.429; most accessible tissue: Minghui63 panicle, score: 95.151	N	N	N	N
vg0719701370	C -> T	LOC_Os07g32970.1	upstream_gene_variant ; 2018.0bp to feature; MODIFIER	silent_mutation	Average:80.429; most accessible tissue: Minghui63 panicle, score: 95.151	N	N	N	N
vg0719701370	C -> T	LOC_Os07g32979.1	upstream_gene_variant ; 2187.0bp to feature; MODIFIER	silent_mutation	Average:80.429; most accessible tissue: Minghui63 panicle, score: 95.151	N	N	N	N
vg0719701370	C -> T	LOC_Os07g32960.1	downstream_gene_variant ; 4483.0bp to feature; MODIFIER	silent_mutation	Average:80.429; most accessible tissue: Minghui63 panicle, score: 95.151	N	N	N	N
vg0719701370	C -> T	LOC_Os07g32970-LOC_Os07g32979	intergenic_region ; MODIFIER	silent_mutation	Average:80.429; most accessible tissue: Minghui63 panicle, score: 95.151	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)
vg0719701370	C	T	-0.02	-0.01	-0.01	0.0	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719701370	NA	3.27E-47	mr1549	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
vg0719701370	NA	3.20E-49	mr1550	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
vg0719701370	NA	3.28E-50	mr1757	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
vg0719701370	NA	4.85E-06	mr1774	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
vg0719701370	NA	1.97E-06	mr1931	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
vg0719701370	NA	1.66E-16	mr1260_2	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
vg0719701370	1.29E-06	8.62E-48	mr1549_2	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
vg0719701370	NA	4.33E-57	mr1550_2	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
vg0719701370	NA	1.17E-38	mr1757_2	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
vg0719701370	NA	7.95E-18	mr1817_2	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