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Detailed information for vg1126520444:

Variant ID: vg1126520444 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26520444
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCACTAAAAAAATTCGCTCCCATGGGGAGTCGAACCCAGGACCTCGGTGCTACTGAGGCTCTTATAACCACTAGGCTACAGGCTCTTTCATGAAAAGTT[A/G]
GAAGATTATGTGTGTAGAAAAGTTTGATGTGATGAAAAAGTTGAAAGTTTGTTTAAAAAAAATTGGATCTAAACACGGTCGTAGTCATGTTTCATATACC

Reverse complement sequence

GGTATATGAAACATGACTACGACCGTGTTTAGATCCAATTTTTTTTAAACAAACTTTCAACTTTTTCATCACATCAAACTTTTCTACACACATAATCTTC[T/C]
AACTTTTCATGAAAGAGCCTGTAGCCTAGTGGTTATAAGAGCCTCAGTAGCACCGAGGTCCTGGGTTCGACTCCCCATGGGAGCGAATTTTTTTAGTGGT

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	46.10%	21.20%	0.28%	32.40%	NA
All Indica	2759	54.50%	23.60%	0.22%	21.67%	NA
All Japonica	1512	36.40%	18.80%	0.33%	44.44%	NA
Aus	269	28.60%	14.90%	0.37%	56.13%	NA
Indica I	595	48.40%	8.60%	0.17%	42.86%	NA
Indica II	465	75.90%	7.10%	0.22%	16.77%	NA
Indica III	913	46.10%	41.30%	0.00%	12.60%	NA
Indica Intermediate	786	56.20%	24.20%	0.51%	19.08%	NA
Temperate Japonica	767	61.90%	18.10%	0.39%	19.56%	NA
Tropical Japonica	504	5.40%	19.40%	0.40%	74.80%	NA
Japonica Intermediate	241	19.90%	19.90%	0.00%	60.17%	NA
VI/Aromatic	96	14.60%	8.30%	0.00%	77.08%	NA
Intermediate	90	40.00%	18.90%	1.11%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126520444	A -> DEL	N	N	silent_mutation	Average:83.155; most accessible tissue: Zhenshan97 panicle, score: 94.594	N	N	N	N
vg1126520444	A -> G	LOC_Os11g43914.1	upstream_gene_variant ; 2385.0bp to feature; MODIFIER	silent_mutation	Average:83.155; most accessible tissue: Zhenshan97 panicle, score: 94.594	N	N	N	N
vg1126520444	A -> G	LOC_Os11g43920.1	downstream_gene_variant ; 1941.0bp to feature; MODIFIER	silent_mutation	Average:83.155; most accessible tissue: Zhenshan97 panicle, score: 94.594	N	N	N	N
vg1126520444	A -> G	LOC_Os11g43934.2	downstream_gene_variant ; 4464.0bp to feature; MODIFIER	silent_mutation	Average:83.155; most accessible tissue: Zhenshan97 panicle, score: 94.594	N	N	N	N
vg1126520444	A -> G	LOC_Os11g43920-LOC_Os11g43934	intergenic_region ; MODIFIER	silent_mutation	Average:83.155; most accessible tissue: Zhenshan97 panicle, score: 94.594	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)
vg1126520444	A	G	0.0	0.0	0.0	-0.01	-0.01	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126520444	NA	1.38E-06	mr1380	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
vg1126520444	NA	1.28E-07	mr1561	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
vg1126520444	NA	1.69E-06	mr1908	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
vg1126520444	NA	4.19E-06	mr1937	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
vg1126520444	NA	7.42E-07	mr1125_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
vg1126520444	NA	5.44E-06	mr1133_2	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