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Detailed information for vg0910516438:

Variant ID: vg0910516438 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 10516438
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCGCGGACGCAGCGGCGGCGGCACGGACACGGAGGCGGTGGCGTGGACGGCGACTGTGGTGGTGCGGAGCCTGTGGTCGGGGCGCATTTTTTTGTTCGTC[C/T]
AGAGGATTTTCGCAGGCGGGCCATTGGGTGATGATTTTCGCAGGCGTTTATCTACAGGCGGTCCTTCCCCCGCCTAGAAAAACTACTTTTGGCCGCCTGC

Reverse complement sequence

GCAGGCGGCCAAAAGTAGTTTTTCTAGGCGGGGGAAGGACCGCCTGTAGATAAACGCCTGCGAAAATCATCACCCAATGGCCCGCCTGCGAAAATCCTCT[G/A]
GACGAACAAAAAAATGCGCCCCGACCACAGGCTCCGCACCACCACAGTCGCCGTCCACGCCACCGCCTCCGTGTCCGTGCCGCCGCCGCTGCGTCCGCGC

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	90.20%	9.30%	0.02%	0.44%	NA
All Indica	2759	87.50%	12.40%	0.04%	0.00%	NA
All Japonica	1512	93.30%	5.40%	0.00%	1.39%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.20%	1.80%	0.00%	0.00%	NA
Indica II	465	68.00%	32.00%	0.00%	0.00%	NA
Indica III	913	91.60%	8.30%	0.11%	0.00%	NA
Indica Intermediate	786	86.40%	13.60%	0.00%	0.00%	NA
Temperate Japonica	767	95.70%	4.30%	0.00%	0.00%	NA
Tropical Japonica	504	89.30%	6.50%	0.00%	4.17%	NA
Japonica Intermediate	241	93.80%	6.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	0.00%	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
vg0910516438	C -> DEL	N	N	silent_mutation	Average:63.268; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0910516438	C -> T	LOC_Os09g17146.1	downstream_gene_variant ; 3501.0bp to feature; MODIFIER	silent_mutation	Average:63.268; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0910516438	C -> T	LOC_Os09g17140-LOC_Os09g17146	intergenic_region ; MODIFIER	silent_mutation	Average:63.268; most accessible tissue: Zhenshan97 young leaf, score: 84.035	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)
vg0910516438	C	T	0.01	0.0	-0.01	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0910516438	NA	2.86E-07	mr1157	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
vg0910516438	NA	4.55E-06	mr1170	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
vg0910516438	NA	7.42E-06	mr1328	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
vg0910516438	NA	8.25E-08	mr1425	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
vg0910516438	NA	1.14E-10	mr1425	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
vg0910516438	NA	2.86E-07	mr1446	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
vg0910516438	NA	2.37E-06	mr1817	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
vg0910516438	NA	7.86E-07	mr1974	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
vg0910516438	NA	1.04E-06	mr1974	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