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Detailed information for vg0806743013:

Variant ID: vg0806743013 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6743013
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAAGGCGAGTGGAACGGCGGCGGCTGGCCAGGGAGAACGAAATTTCCCAACTAATCTTCACCATTTTCCGTGCACATGCTTTTCAAACTAATCTTTATT[A/G]
TTTTCCGCGCGCACACTTTTTAAACCGCTAAATATTGCCTTTTTTATAAAAAAAATTATTGAAAAGTTGCTTGAAAAAATCACTTTGTTCCATTTTTTTT

Reverse complement sequence

AAAAAAAATGGAACAAAGTGATTTTTTCAAGCAACTTTTCAATAATTTTTTTTATAAAAAAGGCAATATTTAGCGGTTTAAAAAGTGTGCGCGCGGAAAA[T/C]
AATAAAGATTAGTTTGAAAAGCATGTGCACGGAAAATGGTGAAGATTAGTTGGGAAATTTCGTTCTCCCTGGCCAGCCGCCGCCGTTCCACTCGCCTTTC

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	66.20%	27.80%	0.02%	5.99%	NA
All Indica	2759	88.40%	1.90%	0.00%	9.75%	NA
All Japonica	1512	19.10%	80.60%	0.07%	0.20%	NA
Aus	269	97.40%	0.70%	0.00%	1.86%	NA
Indica I	595	99.70%	0.20%	0.00%	0.17%	NA
Indica II	465	90.80%	4.10%	0.00%	5.16%	NA
Indica III	913	80.10%	0.50%	0.00%	19.39%	NA
Indica Intermediate	786	88.00%	3.40%	0.00%	8.52%	NA
Temperate Japonica	767	31.20%	68.70%	0.13%	0.00%	NA
Tropical Japonica	504	3.40%	96.00%	0.00%	0.60%	NA
Japonica Intermediate	241	13.70%	86.30%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	3.10%	0.00%	1.04%	NA
Intermediate	90	53.30%	41.10%	0.00%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806743013	A -> G	LOC_Os08g11490.1	upstream_gene_variant ; 135.0bp to feature; MODIFIER	silent_mutation	Average:85.336; most accessible tissue: Callus, score: 93.047	N	N	N	N
vg0806743013	A -> G	LOC_Os08g11480.1	downstream_gene_variant ; 3327.0bp to feature; MODIFIER	silent_mutation	Average:85.336; most accessible tissue: Callus, score: 93.047	N	N	N	N
vg0806743013	A -> G	LOC_Os08g11500.1	downstream_gene_variant ; 2831.0bp to feature; MODIFIER	silent_mutation	Average:85.336; most accessible tissue: Callus, score: 93.047	N	N	N	N
vg0806743013	A -> G	LOC_Os08g11490-LOC_Os08g11500	intergenic_region ; MODIFIER	silent_mutation	Average:85.336; most accessible tissue: Callus, score: 93.047	N	N	N	N
vg0806743013	A -> DEL	N	N	silent_mutation	Average:85.336; most accessible tissue: Callus, score: 93.047	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)
vg0806743013	A	G	-0.21	-0.29	-0.25	-0.11	-0.18	-0.17

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806743013	NA	7.59E-08	mr1162	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
vg0806743013	NA	1.18E-09	mr1905	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
vg0806743013	1.93E-07	NA	mr1071_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
vg0806743013	NA	1.57E-06	mr1071_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
vg0806743013	1.64E-06	NA	mr1080_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
vg0806743013	NA	3.39E-06	mr1080_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
vg0806743013	NA	7.90E-06	mr1100_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
vg0806743013	6.80E-09	NA	mr1203_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
vg0806743013	NA	6.45E-07	mr1203_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
vg0806743013	NA	7.45E-06	mr1613_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
vg0806743013	NA	5.05E-09	mr1705_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
vg0806743013	NA	1.89E-07	mr1821_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
vg0806743013	NA	2.88E-19	mr1945_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