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Detailed information for vg0102400224:

Variant ID: vg0102400224 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2400224
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGTGGTCGATATCAAGAGGATGCAATGGACTTAACAGAGAAAGGAAACAAGCCAGATACATAGAATAGACGTAAGGGAGAGAATATAAACTTTCTATATT[C/T]
GGCCCAAACCTGAAAGGGAGGATTTTGATTCCTTTTTCCAATTAAATAATTGTTAAATGAGGTTTGTATTATTAAAATTAGCAATTAAGCTCTGAAAATT

Reverse complement sequence

AATTTTCAGAGCTTAATTGCTAATTTTAATAATACAAACCTCATTTAACAATTATTTAATTGGAAAAAGGAATCAAAATCCTCCCTTTCAGGTTTGGGCC[G/A]
AATATAGAAAGTTTATATTCTCTCCCTTACGTCTATTCTATGTATCTGGCTTGTTTCCTTTCTCTGTTAAGTCCATTGCATCCTCTTGATATCGACCACA

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	78.10%	0.90%	0.06%	20.88%	NA
All Indica	2759	72.40%	0.00%	0.07%	27.55%	NA
All Japonica	1512	83.70%	2.80%	0.07%	13.43%	NA
Aus	269	94.10%	0.00%	0.00%	5.95%	NA
Indica I	595	34.30%	0.00%	0.00%	65.71%	NA
Indica II	465	94.40%	0.00%	0.00%	5.59%	NA
Indica III	913	81.40%	0.00%	0.22%	18.40%	NA
Indica Intermediate	786	77.70%	0.00%	0.00%	22.26%	NA
Temperate Japonica	767	95.70%	0.10%	0.13%	4.04%	NA
Tropical Japonica	504	74.20%	1.60%	0.00%	24.21%	NA
Japonica Intermediate	241	65.10%	14.10%	0.00%	20.75%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	91.10%	0.00%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0102400224	C -> T	LOC_Os01g05130.1	upstream_gene_variant ; 3046.0bp to feature; MODIFIER	silent_mutation	Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833	N	N	N	N
vg0102400224	C -> T	LOC_Os01g05105.1	downstream_gene_variant ; 1932.0bp to feature; MODIFIER	silent_mutation	Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833	N	N	N	N
vg0102400224	C -> T	LOC_Os01g05120.1	downstream_gene_variant ; 721.0bp to feature; MODIFIER	silent_mutation	Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833	N	N	N	N
vg0102400224	C -> T	LOC_Os01g05105-LOC_Os01g05120	intergenic_region ; MODIFIER	silent_mutation	Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833	N	N	N	N
vg0102400224	C -> DEL	N	N	silent_mutation	Average:49.129; most accessible tissue: Minghui63 panicle, score: 90.833	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)
vg0102400224	C	T	-0.13	-0.13	-0.11	-0.1	-0.11	-0.11

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102400224	NA	7.00E-06	mr1064	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
vg0102400224	NA	1.70E-06	mr1219	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
vg0102400224	9.09E-07	9.09E-07	mr1849	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
vg0102400224	NA	1.81E-06	mr1904	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