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Detailed information for vg1107414104:

Variant ID: vg1107414104 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 7414104
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATGATTGTATTCTCAAGGTTTTCTTGTACTCTCATATTTTTTAAGAGTGAGTTGCATATTGGGCTAGTTATTATTGCTAAAGTTTCACTTTGGGCTATG[A/G]
CACATCTCATGTTTTCACTTTAGCACAGGGTTTTTTACCTTTAGTTCCATACTAGACAACCCTATCTTCAACGTCTCCTACTTGTTCCAACTCAGTCACT

Reverse complement sequence

AGTGACTGAGTTGGAACAAGTAGGAGACGTTGAAGATAGGGTTGTCTAGTATGGAACTAAAGGTAAAAAACCCTGTGCTAAAGTGAAAACATGAGATGTG[T/C]
CATAGCCCAAAGTGAAACTTTAGCAATAATAACTAGCCCAATATGCAACTCACTCTTAAAAAATATGAGAGTACAAGAAAACCTTGAGAATACAATCATA

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	61.00%	35.80%	0.87%	2.37%	NA
All Indica	2759	95.30%	3.40%	0.62%	0.72%	NA
All Japonica	1512	5.80%	90.10%	0.53%	3.57%	NA
Aus	269	42.80%	39.80%	4.83%	12.64%	NA
Indica I	595	95.80%	2.50%	1.18%	0.50%	NA
Indica II	465	99.10%	0.40%	0.00%	0.43%	NA
Indica III	913	96.90%	2.20%	0.11%	0.77%	NA
Indica Intermediate	786	90.60%	7.30%	1.15%	1.02%	NA
Temperate Japonica	767	3.70%	95.20%	0.13%	1.04%	NA
Tropical Japonica	504	8.30%	87.70%	1.19%	2.78%	NA
Japonica Intermediate	241	7.50%	78.80%	0.41%	13.28%	NA
VI/Aromatic	96	2.10%	96.90%	0.00%	1.04%	NA
Intermediate	90	55.60%	37.80%	3.33%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1107414104	A -> DEL	N	N	silent_mutation	Average:68.61; most accessible tissue: Minghui63 flower, score: 85.291	N	N	N	N
vg1107414104	A -> G	LOC_Os11g13520.1	upstream_gene_variant ; 867.0bp to feature; MODIFIER	silent_mutation	Average:68.61; most accessible tissue: Minghui63 flower, score: 85.291	N	N	N	N
vg1107414104	A -> G	LOC_Os11g13520-LOC_Os11g13530	intergenic_region ; MODIFIER	silent_mutation	Average:68.61; most accessible tissue: Minghui63 flower, score: 85.291	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)
vg1107414104	A	G	0.01	0.01	0.01	0.01	0.02	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1107414104	NA	2.91E-18	mr1552	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
vg1107414104	7.60E-06	7.60E-06	mr1173_2	Ind_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
vg1107414104	NA	2.27E-08	mr1940_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