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Detailed information for vg1125639786:

Variant ID: vg1125639786 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25639786
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAGGTGCCGGTTCGTAATAAGAACCGACACCTATCTTACGGCTACATAGGTGCCGTTTTATCCTAATAAACCGGCACCTATGTGATTTTTAATAGGAAC[T/C]
GGCACCTATGTGGTGGCTTCCGTCGGAAGGAAACTAAATAGGTGCCGGTTCATAACATGAACCGACACCTATATCCCCCAAGTCTATATATACCCTTTGT

Reverse complement sequence

ACAAAGGGTATATATAGACTTGGGGGATATAGGTGTCGGTTCATGTTATGAACCGGCACCTATTTAGTTTCCTTCCGACGGAAGCCACCACATAGGTGCC[A/G]
GTTCCTATTAAAAATCACATAGGTGCCGGTTTATTAGGATAAAACGGCACCTATGTAGCCGTAAGATAGGTGTCGGTTCTTATTACGAACCGGCACCTAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	13.40%	12.50%	8.23%	65.83%	NA
All Indica	2759	19.50%	2.60%	11.89%	66.00%	NA
All Japonica	1512	4.70%	29.70%	1.79%	63.82%	NA
Aus	269	3.30%	21.20%	8.18%	67.29%	NA
Indica I	595	34.30%	3.20%	7.90%	54.62%	NA
Indica II	465	20.00%	2.40%	8.39%	69.25%	NA
Indica III	913	16.00%	1.50%	16.32%	66.16%	NA
Indica Intermediate	786	12.10%	3.60%	11.83%	72.52%	NA
Temperate Japonica	767	1.20%	54.10%	1.83%	42.89%	NA
Tropical Japonica	504	7.50%	1.40%	1.39%	89.68%	NA
Japonica Intermediate	241	10.00%	11.20%	2.49%	76.35%	NA
VI/Aromatic	96	0.00%	4.20%	3.12%	92.71%	NA
Intermediate	90	17.80%	11.10%	10.00%	61.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125639786	T -> DEL	N	N	silent_mutation	Average:48.835; most accessible tissue: Minghui63 young leaf, score: 96.99	N	N	N	N
vg1125639786	T -> C	LOC_Os11g42600.1	upstream_gene_variant ; 452.0bp to feature; MODIFIER	silent_mutation	Average:48.835; most accessible tissue: Minghui63 young leaf, score: 96.99	N	N	N	N
vg1125639786	T -> C	LOC_Os11g42590.1	downstream_gene_variant ; 854.0bp to feature; MODIFIER	silent_mutation	Average:48.835; most accessible tissue: Minghui63 young leaf, score: 96.99	N	N	N	N
vg1125639786	T -> C	LOC_Os11g42590-LOC_Os11g42600	intergenic_region ; MODIFIER	silent_mutation	Average:48.835; most accessible tissue: Minghui63 young leaf, score: 96.99	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)
vg1125639786	T	C	0.0	0.01	0.01	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125639786	NA	1.74E-07	mr1133	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
vg1125639786	NA	1.08E-10	mr1191	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
vg1125639786	6.01E-06	1.05E-07	mr1191	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
vg1125639786	4.99E-07	1.38E-14	mr1644	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
vg1125639786	1.08E-08	1.70E-11	mr1644	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
vg1125639786	NA	2.12E-17	mr1191_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
vg1125639786	NA	1.06E-09	mr1191_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
vg1125639786	NA	5.39E-06	mr1561_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
vg1125639786	NA	1.88E-06	mr1875_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
vg1125639786	NA	3.77E-06	mr1908_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
vg1125639786	NA	6.22E-06	mr1996_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