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Detailed information for vg1128496200:

Variant ID: vg1128496200 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28496200
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTCATAGAGCTCATTCAATTCCATTACGTACATTAGCCCTCATAGCATGGAAAATAGTCATTCAATTTCACACATTGTACCATTATACATGACAACAGA[G/A]
CACTTCTTTCCTCCCTATACTATAAACAAAAACAACCAGAAAAGCAAATTCTTCTAGCTGTGCATTCACTTTTCCATTTCTGATGCCATGGGTCTTATTC

Reverse complement sequence

GAATAAGACCCATGGCATCAGAAATGGAAAAGTGAATGCACAGCTAGAAGAATTTGCTTTTCTGGTTGTTTTTGTTTATAGTATAGGGAGGAAAGAAGTG[C/T]
TCTGTTGTCATGTATAATGGTACAATGTGTGAAATTGAATGACTATTTTCCATGCTATGAGGGCTAATGTACGTAATGGAATTGAATGAGCTCTATGAAG

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	41.10%	13.40%	0.87%	44.60%	NA
All Indica	2759	35.70%	9.40%	0.69%	54.26%	NA
All Japonica	1512	45.80%	23.50%	0.99%	29.70%	NA
Aus	269	47.60%	1.10%	1.86%	49.44%	NA
Indica I	595	59.00%	5.70%	0.84%	34.45%	NA
Indica II	465	27.10%	1.10%	0.86%	70.97%	NA
Indica III	913	29.00%	12.40%	0.22%	58.38%	NA
Indica Intermediate	786	30.80%	13.60%	1.02%	54.58%	NA
Temperate Japonica	767	51.10%	9.50%	1.56%	37.81%	NA
Tropical Japonica	504	35.70%	49.20%	0.40%	14.68%	NA
Japonica Intermediate	241	50.20%	14.10%	0.41%	35.27%	NA
VI/Aromatic	96	88.50%	5.20%	0.00%	6.25%	NA
Intermediate	90	60.00%	12.20%	2.22%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128496200	G -> A	LOC_Os11g47370.1	upstream_gene_variant ; 503.0bp to feature; MODIFIER	silent_mutation	Average:81.515; most accessible tissue: Callus, score: 95.122	N	N	N	N
vg1128496200	G -> A	LOC_Os11g47360.1	downstream_gene_variant ; 2300.0bp to feature; MODIFIER	silent_mutation	Average:81.515; most accessible tissue: Callus, score: 95.122	N	N	N	N
vg1128496200	G -> A	LOC_Os11g47360-LOC_Os11g47370	intergenic_region ; MODIFIER	silent_mutation	Average:81.515; most accessible tissue: Callus, score: 95.122	N	N	N	N
vg1128496200	G -> DEL	N	N	silent_mutation	Average:81.515; most accessible tissue: Callus, score: 95.122	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)
vg1128496200	G	A	0.0	-0.01	-0.02	-0.01	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128496200	NA	4.86E-08	mr1170	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
vg1128496200	NA	3.55E-06	mr1546	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
vg1128496200	NA	8.83E-06	mr1660	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