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Detailed information for vg1018943301:

Variant ID: vg1018943301 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 18943301
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGCACAGTGCTGGAGTCGCTGGCCACTGCGGTTCCGCGTTTTGGAACCGCGGGACCGTCGCGATTCCGCGTTTTGGAGCTGCCGGACCATGACGGTTCC[G/A]
CGCAGGATCGTCGGTCCCGTATTTTGAATCTGCGGAACCGTCGCTGTCCCGCGTTTCCGTTTCGCGGGATGCGTATATTTTTATAAAACCTCTCCATGCA

Reverse complement sequence

TGCATGGAGAGGTTTTATAAAAATATACGCATCCCGCGAAACGGAAACGCGGGACAGCGACGGTTCCGCAGATTCAAAATACGGGACCGACGATCCTGCG[C/T]
GGAACCGTCATGGTCCGGCAGCTCCAAAACGCGGAATCGCGACGGTCCCGCGGTTCCAAAACGCGGAACCGCAGTGGCCAGCGACTCCAGCACTGTGCAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.00%	6.60%	1.31%	0.00%	NA
All Indica	2759	97.60%	1.60%	0.87%	0.00%	NA
All Japonica	1512	80.00%	17.70%	2.25%	0.00%	NA
Aus	269	99.30%	0.00%	0.74%	0.00%	NA
Indica I	595	94.10%	3.00%	2.86%	0.00%	NA
Indica II	465	97.40%	2.20%	0.43%	0.00%	NA
Indica III	913	99.20%	0.80%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.00%	0.64%	0.00%	NA
Temperate Japonica	767	98.00%	1.20%	0.78%	0.00%	NA
Tropical Japonica	504	47.40%	47.40%	5.16%	0.00%	NA
Japonica Intermediate	241	90.90%	8.30%	0.83%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	3.30%	2.22%	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
vg1018943301	G -> A	LOC_Os10g35436.1	downstream_gene_variant ; 728.0bp to feature; MODIFIER	silent_mutation	Average:89.194; most accessible tissue: Zhenshan97 panicle, score: 98.298	N	N	N	N
vg1018943301	G -> A	LOC_Os10g35436-LOC_Os10g35440	intergenic_region ; MODIFIER	silent_mutation	Average:89.194; most accessible tissue: Zhenshan97 panicle, score: 98.298	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)
vg1018943301	G	A	-0.01	-0.01	-0.03	-0.05	-0.03	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1018943301	NA	8.05E-17	mr1771	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
vg1018943301	NA	1.13E-14	mr1784	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
vg1018943301	NA	1.21E-07	mr1800	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
vg1018943301	NA	1.25E-06	mr1363_2	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
vg1018943301	NA	7.79E-08	mr1526_2	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
vg1018943301	NA	3.87E-10	mr1705_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
vg1018943301	NA	2.27E-13	mr1771_2	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
vg1018943301	NA	3.81E-14	mr1784_2	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
vg1018943301	1.77E-07	3.62E-14	mr1800_2	Jap_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
vg1018943301	NA	1.13E-12	mr1862_2	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