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Detailed information for vg0808427097:

Variant ID: vg0808427097 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 8427097
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCTGTATATCTATAGTTGGTGGAGATGCTAGCTAGAACACTACTAAGAAAACCATTTCTGCAGACGAAACCCTTCTATTTTTCAGACGGATGTTTATTTT[G/A]
AACCGTATATACATCCTCTTATGAAATGCTTATTGCTTTCTCGCAAGTACAAAACGGTACGGTGTCAATTAATCCTTGGTTGATATCAACGGAGCTATGG

Reverse complement sequence

CCATAGCTCCGTTGATATCAACCAAGGATTAATTGACACCGTACCGTTTTGTACTTGCGAGAAAGCAATAAGCATTTCATAAGAGGATGTATATACGGTT[C/T]
AAAATAAACATCCGTCTGAAAAATAGAAGGGTTTCGTCTGCAGAAATGGTTTTCTTAGTAGTGTTCTAGCTAGCATCTCCACCAACTATAGATATACAGC

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	90.30%	9.70%	0.02%	0.00%	NA
All Indica	2759	88.50%	11.50%	0.04%	0.00%	NA
All Japonica	1512	91.40%	8.60%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.10%	6.90%	0.00%	0.00%	NA
Indica II	465	95.10%	4.90%	0.00%	0.00%	NA
Indica III	913	78.10%	21.80%	0.11%	0.00%	NA
Indica Intermediate	786	93.30%	6.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	82.70%	17.30%	0.00%	0.00%	NA
Japonica Intermediate	241	85.10%	14.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0808427097	G -> A	LOC_Os08g14090.1	upstream_gene_variant ; 4005.0bp to feature; MODIFIER	silent_mutation	Average:79.677; most accessible tissue: Zhenshan97 root, score: 95.697	N	N	N	N
vg0808427097	G -> A	LOC_Os08g14070.1	downstream_gene_variant ; 1806.0bp to feature; MODIFIER	silent_mutation	Average:79.677; most accessible tissue: Zhenshan97 root, score: 95.697	N	N	N	N
vg0808427097	G -> A	LOC_Os08g14070-LOC_Os08g14090	intergenic_region ; MODIFIER	silent_mutation	Average:79.677; most accessible tissue: Zhenshan97 root, score: 95.697	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)
vg0808427097	G	A	0.11	-0.02	-0.02	-0.02	-0.03	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0808427097	NA	8.95E-06	mr1807	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
vg0808427097	7.28E-06	7.28E-06	mr1192_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
vg0808427097	7.13E-06	1.94E-06	mr1267_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
vg0808427097	NA	8.96E-06	mr1267_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
vg0808427097	NA	7.36E-06	mr1312_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
vg0808427097	4.54E-06	4.54E-06	mr1373_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
vg0808427097	9.05E-06	9.58E-07	mr1397_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
vg0808427097	3.20E-07	2.30E-07	mr1663_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
vg0808427097	2.98E-06	2.98E-06	mr1663_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
vg0808427097	2.95E-06	2.95E-06	mr1674_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
vg0808427097	6.86E-06	6.86E-06	mr1688_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
vg0808427097	3.91E-07	3.91E-07	mr1822_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
vg0808427097	NA	5.91E-06	mr1843_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
vg0808427097	9.92E-07	9.50E-07	mr1982_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