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Detailed information for vg0724383895:

Variant ID: vg0724383895 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 24383895
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

ACTATGACCCTAGTTTCATCCATTTTCTGGTATTCAGAATTCTTTCTCGAATTGTGATCCCTTTTGACCATTACATTGGGAAACTCCTCTATCCTAAAGA[T/C]
ATTTTTTTTCTCAACAACTCAACACACAGACTATTGTATGAGGACTCAATTTTCATAACTCATTTGGCCGATAGAACAGTGTTCAGCATTCTAGTTTTAG

Reverse complement sequence

CTAAAACTAGAATGCTGAACACTGTTCTATCGGCCAAATGAGTTATGAAAATTGAGTCCTCATACAATAGTCTGTGTGTTGAGTTGTTGAGAAAAAAAAT[A/G]
TCTTTAGGATAGAGGAGTTTCCCAATGTAATGGTCAAAAGGGATCACAATTCGAGAAAGAATTCTGAATACCAGAAAATGGATGAAACTAGGGTCATAGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.20%	3.90%	8.13%	3.77%	NA
All Indica	2759	88.90%	0.30%	7.32%	3.44%	NA
All Japonica	1512	85.80%	11.50%	2.58%	0.13%	NA
Aus	269	34.20%	0.00%	41.26%	24.54%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	91.80%	1.50%	6.02%	0.65%	NA
Indica III	913	83.70%	0.00%	10.62%	5.70%	NA
Indica Intermediate	786	85.20%	0.10%	9.54%	5.09%	NA
Temperate Japonica	767	74.30%	21.40%	4.30%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	93.40%	3.30%	2.49%	0.83%	NA
VI/Aromatic	96	62.50%	0.00%	25.00%	12.50%	NA
Intermediate	90	84.40%	3.30%	8.89%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0724383895	T -> DEL	N	N	silent_mutation	Average:48.888; most accessible tissue: Zhenshan97 root, score: 82.549	N	N	N	N
vg0724383895	T -> C	LOC_Os07g40690.1	upstream_gene_variant ; 513.0bp to feature; MODIFIER	silent_mutation	Average:48.888; most accessible tissue: Zhenshan97 root, score: 82.549	N	N	N	N
vg0724383895	T -> C	LOC_Os07g40680-LOC_Os07g40690	intergenic_region ; MODIFIER	silent_mutation	Average:48.888; most accessible tissue: Zhenshan97 root, score: 82.549	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)
vg0724383895	T	C	-0.03	-0.02	-0.01	-0.02	-0.01	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0724383895	9.89E-07	8.49E-07	mr1138	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
vg0724383895	9.17E-12	2.53E-12	mr1354	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
vg0724383895	3.20E-07	1.49E-08	mr1829	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
vg0724383895	NA	2.83E-07	mr1902	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
vg0724383895	NA	5.70E-06	mr1138_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
vg0724383895	5.31E-06	5.31E-06	mr1181_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
vg0724383895	NA	1.78E-06	mr1182_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
vg0724383895	5.65E-13	1.67E-14	mr1354_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
vg0724383895	NA	1.12E-06	mr1567_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
vg0724383895	6.47E-06	5.79E-08	mr1829_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
vg0724383895	3.36E-07	2.88E-10	mr1902_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