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Detailed information for vg1001393945:

Variant ID: vg1001393945 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 1393945
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGGTTAGGCTTTTTGGTCTTCTATGAGCTATATTTTAAGTGTTTATATATACCCCGGGGCCCTACGGGTCACCCTCGGGGGTGAAATGTTTTCTCCTGTC[C/T]
CCTCCCCACCCAAATACGGACCCTCCGTCCCCAATAACCCCGCGGGTTGAAAATCACACCCACCCCCGATCCCGCGGAGGAAATTGCCATCCCTAGACAA

Reverse complement sequence

TTGTCTAGGGATGGCAATTTCCTCCGCGGGATCGGGGGTGGGTGTGATTTTCAACCCGCGGGGTTATTGGGGACGGAGGGTCCGTATTTGGGTGGGGAGG[G/A]
GACAGGAGAAAACATTTCACCCCCGAGGGTGACCCGTAGGGCCCCGGGGTATATATAAACACTTAAAATATAGCTCATAGAAGACCAAAAAGCCTAACCT

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	84.90%	12.60%	0.11%	2.37%	NA
All Indica	2759	94.50%	1.30%	0.14%	4.06%	NA
All Japonica	1512	69.90%	30.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.70%	0.30%	0.00%	1.01%	NA
Indica II	465	95.50%	2.80%	0.00%	1.72%	NA
Indica III	913	91.90%	0.10%	0.11%	7.89%	NA
Indica Intermediate	786	93.60%	2.70%	0.38%	3.31%	NA
Temperate Japonica	767	75.60%	24.40%	0.00%	0.00%	NA
Tropical Japonica	504	78.40%	21.60%	0.00%	0.00%	NA
Japonica Intermediate	241	34.00%	66.00%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
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
vg1001393945	C -> T	LOC_Os10g03300.1	upstream_gene_variant ; 1987.0bp to feature; MODIFIER	silent_mutation	Average:89.336; most accessible tissue: Zhenshan97 young leaf, score: 99.517	N	N	N	N
vg1001393945	C -> T	LOC_Os10g03280.1	downstream_gene_variant ; 4759.0bp to feature; MODIFIER	silent_mutation	Average:89.336; most accessible tissue: Zhenshan97 young leaf, score: 99.517	N	N	N	N
vg1001393945	C -> T	LOC_Os10g03290.1	downstream_gene_variant ; 2116.0bp to feature; MODIFIER	silent_mutation	Average:89.336; most accessible tissue: Zhenshan97 young leaf, score: 99.517	N	N	N	N
vg1001393945	C -> T	LOC_Os10g03290-LOC_Os10g03300	intergenic_region ; MODIFIER	silent_mutation	Average:89.336; most accessible tissue: Zhenshan97 young leaf, score: 99.517	N	N	N	N
vg1001393945	C -> DEL	N	N	silent_mutation	Average:89.336; most accessible tissue: Zhenshan97 young leaf, score: 99.517	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)
vg1001393945	C	T	0.08	0.02	0.04	-0.08	0.0	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1001393945	NA	7.75E-08	mr1174	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
vg1001393945	NA	5.16E-06	mr1174	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
vg1001393945	NA	2.55E-06	mr1304	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
vg1001393945	4.51E-07	NA	mr1486	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
vg1001393945	NA	1.17E-08	mr1514	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
vg1001393945	NA	4.42E-06	mr1548	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
vg1001393945	NA	1.04E-08	mr1570	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
vg1001393945	4.17E-06	NA	mr1845	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
vg1001393945	NA	6.69E-06	mr1174_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
vg1001393945	3.80E-11	NA	mr1486_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
vg1001393945	1.11E-08	NA	mr1486_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