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Detailed information for vg0335115022:

Variant ID: vg0335115022 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 35115022
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAAGCCTAATTAATCCGTCATAGCACATGTGGGTTACTGTAACACATATGGCTAATCATGGATTAATTAGGCTCAAAAGATTCGTATCGCGATTTTCAT[A/G]
CACACTGTGCAATTAGTTTTTTATTTTATTTATATTTAATATATACTTTATACATATGTCCAAAGATTCGATGTGATGTTTTTGGGATTTTTTTTCTTTT

Reverse complement sequence

AAAAGAAAAAAAATCCCAAAAACATCACATCGAATCTTTGGACATATGTATAAAGTATATATTAAATATAAATAAAATAAAAAACTAATTGCACAGTGTG[T/C]
ATGAAAATCGCGATACGAATCTTTTGAGCCTAATTAATCCATGATTAGCCATATGTGTTACAGTAACCCACATGTGCTATGACGGATTAATTAGGCTTAA

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	81.70%	14.50%	3.81%	0.00%	NA
All Indica	2759	94.20%	2.60%	3.15%	0.00%	NA
All Japonica	1512	54.40%	39.80%	5.75%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	83.90%	6.90%	9.24%	0.00%	NA
Indica II	465	95.10%	2.60%	2.37%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	95.20%	2.20%	2.67%	0.00%	NA
Temperate Japonica	767	28.00%	63.20%	8.74%	0.00%	NA
Tropical Japonica	504	89.90%	8.10%	1.98%	0.00%	NA
Japonica Intermediate	241	64.30%	31.50%	4.15%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	83.30%	11.10%	5.56%	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
vg0335115022	A -> G	LOC_Os03g61930.1	upstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:87.53; most accessible tissue: Callus, score: 93.932	N	N	N	N
vg0335115022	A -> G	LOC_Os03g61940.1	upstream_gene_variant ; 722.0bp to feature; MODIFIER	silent_mutation	Average:87.53; most accessible tissue: Callus, score: 93.932	N	N	N	N
vg0335115022	A -> G	LOC_Os03g61950.1	upstream_gene_variant ; 247.0bp to feature; MODIFIER	silent_mutation	Average:87.53; most accessible tissue: Callus, score: 93.932	N	N	N	N
vg0335115022	A -> G	LOC_Os03g61930.3	upstream_gene_variant ; 3615.0bp to feature; MODIFIER	silent_mutation	Average:87.53; most accessible tissue: Callus, score: 93.932	N	N	N	N
vg0335115022	A -> G	LOC_Os03g61930.2	upstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:87.53; most accessible tissue: Callus, score: 93.932	N	N	N	N
vg0335115022	A -> G	LOC_Os03g61930.4	upstream_gene_variant ; 2489.0bp to feature; MODIFIER	silent_mutation	Average:87.53; most accessible tissue: Callus, score: 93.932	N	N	N	N
vg0335115022	A -> G	LOC_Os03g61950.2	upstream_gene_variant ; 247.0bp to feature; MODIFIER	silent_mutation	Average:87.53; most accessible tissue: Callus, score: 93.932	N	N	N	N
vg0335115022	A -> G	LOC_Os03g61940-LOC_Os03g61950	intergenic_region ; MODIFIER	silent_mutation	Average:87.53; most accessible tissue: Callus, score: 93.932	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)
vg0335115022	A	G	-0.06	-0.05	-0.04	-0.03	-0.03	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0335115022	NA	3.59E-08	mr1002	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
vg0335115022	NA	2.05E-07	mr1002	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
vg0335115022	7.58E-07	6.19E-15	mr1002_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
vg0335115022	NA	8.39E-12	mr1002_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
vg0335115022	NA	8.41E-06	mr1173_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
vg0335115022	NA	4.00E-13	mr1182_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
vg0335115022	NA	1.07E-06	mr1182_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
vg0335115022	NA	5.90E-10	mr1282_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
vg0335115022	1.30E-06	NA	mr1691_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