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Detailed information for vg0328679653:

Variant ID: vg0328679653 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 28679653
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAACTCATAACAAAATAAATTATAATTACGTAAATTTTTTTAATAAGACGAATGGTCAAACATGTGAGAAAAAGTCAACGGCGTTATCTATTAAAAAACG[A/G]
AGGTAGTATTAAATATAGACTACTTACAAAACTAATTACATAAATGAAAACTAATTCGTGAGATAAATTTTTTAAGCCTAATTAATCTATAATTAGAGAA

Reverse complement sequence

TTCTCTAATTATAGATTAATTAGGCTTAAAAAATTTATCTCACGAATTAGTTTTCATTTATGTAATTAGTTTTGTAAGTAGTCTATATTTAATACTACCT[T/C]
CGTTTTTTAATAGATAACGCCGTTGACTTTTTCTCACATGTTTGACCATTCGTCTTATTAAAAAAATTTACGTAATTATAATTTATTTTGTTATGAGTTG

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	84.20%	7.60%	7.93%	0.23%	NA
All Indica	2759	92.00%	1.60%	6.45%	0.00%	NA
All Japonica	1512	66.00%	20.60%	12.63%	0.73%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	75.80%	5.40%	18.82%	0.00%	NA
Indica II	465	96.80%	0.90%	2.37%	0.00%	NA
Indica III	913	99.60%	0.00%	0.44%	0.00%	NA
Indica Intermediate	786	92.60%	0.90%	6.49%	0.00%	NA
Temperate Japonica	767	41.30%	39.10%	18.12%	1.43%	NA
Tropical Japonica	504	94.80%	0.60%	4.56%	0.00%	NA
Japonica Intermediate	241	84.20%	3.70%	12.03%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	6.70%	6.67%	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
vg0328679653	A -> DEL	N	N	silent_mutation	Average:64.211; most accessible tissue: Minghui63 flag leaf, score: 93.28	N	N	N	N
vg0328679653	A -> G	LOC_Os03g50300.1	downstream_gene_variant ; 604.0bp to feature; MODIFIER	silent_mutation	Average:64.211; most accessible tissue: Minghui63 flag leaf, score: 93.28	N	N	N	N
vg0328679653	A -> G	LOC_Os03g50300-LOC_Os03g50310	intergenic_region ; MODIFIER	silent_mutation	Average:64.211; most accessible tissue: Minghui63 flag leaf, score: 93.28	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)
vg0328679653	A	G	0.01	0.01	0.01	0.01	0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0328679653	3.32E-06	NA	mr1382	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
vg0328679653	NA	1.43E-07	mr1617	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
vg0328679653	NA	1.36E-07	mr1804	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
vg0328679653	NA	8.69E-06	mr1955	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
vg0328679653	NA	3.19E-06	mr1977	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
vg0328679653	2.87E-07	NA	mr1310_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
vg0328679653	NA	4.44E-08	mr1310_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
vg0328679653	NA	4.24E-14	mr1959_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
vg0328679653	NA	6.77E-07	mr1959_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