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Detailed information for vg0705219339:

Variant ID: vg0705219339 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 5219339
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTTTCCATGGGCCCTACCCAAACGAAACCTCCAGATGGGCCGTACTCTCGGCTGCCCATGGGCCGGGCCCCAACGGAACGCACGGATAGGTTGGGCTTG[G/T]
GCTGGATTGGACATGACGCCATTTGAAGGCCCATCCAGACAGCGAGAGCGGCGCCGCGGCCGCTACTTCTACCCGCCGCCGCCTCTCCACTCCACTCCAC

Reverse complement sequence

GTGGAGTGGAGTGGAGAGGCGGCGGCGGGTAGAAGTAGCGGCCGCGGCGCCGCTCTCGCTGTCTGGATGGGCCTTCAAATGGCGTCATGTCCAATCCAGC[C/A]
CAAGCCCAACCTATCCGTGCGTTCCGTTGGGGCCCGGCCCATGGGCAGCCGAGAGTACGGCCCATCTGGAGGTTTCGTTTGGGTAGGGCCCATGGAAACC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.10%	4.80%	0.04%	0.00%	NA
All Indica	2759	98.90%	1.00%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	26.40%	73.20%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	98.70%	1.20%	0.11%	0.00%	NA
Indica Intermediate	786	98.00%	2.00%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0705219339	G -> T	LOC_Os07g09800.1	upstream_gene_variant ; 2243.0bp to feature; MODIFIER	silent_mutation	Average:87.653; most accessible tissue: Minghui63 young leaf, score: 99.217	N	N	N	N
vg0705219339	G -> T	LOC_Os07g09814.1	upstream_gene_variant ; 99.0bp to feature; MODIFIER	silent_mutation	Average:87.653; most accessible tissue: Minghui63 young leaf, score: 99.217	N	N	N	N
vg0705219339	G -> T	LOC_Os07g09814.3	upstream_gene_variant ; 99.0bp to feature; MODIFIER	silent_mutation	Average:87.653; most accessible tissue: Minghui63 young leaf, score: 99.217	N	N	N	N
vg0705219339	G -> T	LOC_Os07g09814.2	upstream_gene_variant ; 99.0bp to feature; MODIFIER	silent_mutation	Average:87.653; most accessible tissue: Minghui63 young leaf, score: 99.217	N	N	N	N
vg0705219339	G -> T	LOC_Os07g09800-LOC_Os07g09814	intergenic_region ; MODIFIER	silent_mutation	Average:87.653; most accessible tissue: Minghui63 young leaf, score: 99.217	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)
vg0705219339	G	T	-0.1	-0.13	-0.09	-0.09	-0.06	-0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0705219339	NA	2.03E-06	mr1126	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
vg0705219339	NA	1.93E-06	mr1365	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
vg0705219339	NA	9.33E-12	mr1522	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
vg0705219339	NA	6.38E-06	mr1545	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
vg0705219339	3.35E-06	1.18E-53	mr1549	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
vg0705219339	7.86E-10	5.27E-66	mr1550	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
vg0705219339	4.64E-06	1.08E-55	mr1757	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
vg0705219339	NA	2.90E-06	mr1774	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
vg0705219339	NA	1.73E-10	mr1931	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
vg0705219339	NA	1.32E-12	mr1409_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
vg0705219339	NA	2.31E-08	mr1510_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
vg0705219339	7.09E-08	7.52E-50	mr1549_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
vg0705219339	2.34E-10	1.77E-74	mr1550_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
vg0705219339	4.83E-07	2.34E-43	mr1757_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
vg0705219339	NA	3.95E-06	mr1762_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