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Detailed information for vg1106885476:

Variant ID: vg1106885476 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6885476
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGATAACTATTGTATATGAATTGGTTATTAAATTGACTATAGTTGATTTGAAGCTAATAGTTGGCTATACTATTAAACTTGCTCTAAAGAGGCTATCTG[A/G]
CCATGTGCTCTGTGTGACATGGCAGTCCTGAGACTCCTGAGCACTACGAGAATCGTTTGCTCTGAACTGAATGTGTATGTATCCCCATACTCAACAAACA

Reverse complement sequence

TGTTTGTTGAGTATGGGGATACATACACATTCAGTTCAGAGCAAACGATTCTCGTAGTGCTCAGGAGTCTCAGGACTGCCATGTCACACAGAGCACATGG[T/C]
CAGATAGCCTCTTTAGAGCAAGTTTAATAGTATAGCCAACTATTAGCTTCAAATCAACTATAGTCAATTTAATAACCAATTCATATACAATAGTTATCTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.50%	31.70%	0.91%	3.94%	NA
All Indica	2759	82.30%	13.70%	0.80%	3.15%	NA
All Japonica	1512	27.10%	65.80%	1.19%	5.95%	NA
Aus	269	94.80%	4.50%	0.00%	0.74%	NA
Indica I	595	82.40%	8.10%	0.17%	9.41%	NA
Indica II	465	95.30%	3.70%	0.65%	0.43%	NA
Indica III	913	77.10%	20.70%	1.42%	0.77%	NA
Indica Intermediate	786	80.80%	15.80%	0.64%	2.80%	NA
Temperate Japonica	767	26.50%	73.10%	0.39%	0.00%	NA
Tropical Japonica	504	29.40%	55.40%	1.39%	13.89%	NA
Japonica Intermediate	241	24.10%	64.30%	3.32%	8.30%	NA
VI/Aromatic	96	12.50%	85.40%	1.04%	1.04%	NA
Intermediate	90	58.90%	32.20%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1106885476	A -> DEL	N	N	silent_mutation	Average:93.753; most accessible tissue: Zhenshan97 flag leaf, score: 96.856	N	N	N	N
vg1106885476	A -> G	LOC_Os11g12340.1	upstream_gene_variant ; 2581.0bp to feature; MODIFIER	silent_mutation	Average:93.753; most accessible tissue: Zhenshan97 flag leaf, score: 96.856	N	N	N	N
vg1106885476	A -> G	LOC_Os11g12340.2	upstream_gene_variant ; 4388.0bp to feature; MODIFIER	silent_mutation	Average:93.753; most accessible tissue: Zhenshan97 flag leaf, score: 96.856	N	N	N	N
vg1106885476	A -> G	LOC_Os11g12330.1	downstream_gene_variant ; 531.0bp to feature; MODIFIER	silent_mutation	Average:93.753; most accessible tissue: Zhenshan97 flag leaf, score: 96.856	N	N	N	N
vg1106885476	A -> G	LOC_Os11g12330-LOC_Os11g12340	intergenic_region ; MODIFIER	silent_mutation	Average:93.753; most accessible tissue: Zhenshan97 flag leaf, score: 96.856	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)
vg1106885476	A	G	0.0	0.0	0.01	0.0	0.0	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106885476	1.54E-06	NA	mr1566_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
vg1106885476	6.18E-06	NA	mr1567_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
vg1106885476	1.31E-06	1.02E-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
vg1106885476	NA	9.41E-06	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