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Detailed information for vg0725636129:

Variant ID: vg0725636129 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 25636129
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

GTTCGTCACAAGACGGACGAAGACCATAATTAAAAATAAGAAATATTGAAATAATAATAGCACAGACTCATGGTCACCGCTGTCGCGGAAGGCCAGACAC[A/G]
GCTGCTACCTACGATGCTACGGTCGTCGATTGGTCTGATGTTGCTCGCTGGTCAATCGTGGTGCTGAGCGACCCCATAGATCTACCCATATCTTCAGAGT

Reverse complement sequence

ACTCTGAAGATATGGGTAGATCTATGGGGTCGCTCAGCACCACGATTGACCAGCGAGCAACATCAGACCAATCGACGACCGTAGCATCGTAGGTAGCAGC[T/C]
GTGTCTGGCCTTCCGCGACAGCGGTGACCATGAGTCTGTGCTATTATTATTTCAATATTTCTTATTTTTAATTATGGTCTTCGTCCGTCTTGTGACGAAC

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	66.60%	33.10%	0.21%	0.04%	NA
All Indica	2759	97.50%	2.30%	0.18%	0.04%	NA
All Japonica	1512	4.20%	95.60%	0.13%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	99.00%	0.80%	0.17%	0.00%	NA
Indica II	465	92.70%	7.10%	0.22%	0.00%	NA
Indica III	913	99.70%	0.20%	0.11%	0.00%	NA
Indica Intermediate	786	96.60%	3.10%	0.25%	0.13%	NA
Temperate Japonica	767	6.90%	92.80%	0.26%	0.00%	NA
Tropical Japonica	504	0.20%	99.80%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	52.20%	43.30%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0725636129	A -> DEL	N	N	silent_mutation	Average:83.429; most accessible tissue: Minghui63 panicle, score: 91.41	N	N	N	N
vg0725636129	A -> G	LOC_Os07g42800.1	upstream_gene_variant ; 574.0bp to feature; MODIFIER	silent_mutation	Average:83.429; most accessible tissue: Minghui63 panicle, score: 91.41	N	N	N	N
vg0725636129	A -> G	LOC_Os07g42810.1	upstream_gene_variant ; 4825.0bp to feature; MODIFIER	silent_mutation	Average:83.429; most accessible tissue: Minghui63 panicle, score: 91.41	N	N	N	N
vg0725636129	A -> G	LOC_Os07g42810.2	upstream_gene_variant ; 4718.0bp to feature; MODIFIER	silent_mutation	Average:83.429; most accessible tissue: Minghui63 panicle, score: 91.41	N	N	N	N
vg0725636129	A -> G	LOC_Os07g42790.1	downstream_gene_variant ; 1563.0bp to feature; MODIFIER	silent_mutation	Average:83.429; most accessible tissue: Minghui63 panicle, score: 91.41	N	N	N	N
vg0725636129	A -> G	LOC_Os07g42790-LOC_Os07g42800	intergenic_region ; MODIFIER	silent_mutation	Average:83.429; most accessible tissue: Minghui63 panicle, score: 91.41	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)
vg0725636129	A	G	-0.02	-0.02	-0.03	-0.02	-0.03	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0725636129	NA	5.56E-23	mr1383	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
vg0725636129	NA	1.22E-21	mr1817	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
vg0725636129	NA	1.11E-09	mr1905	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
vg0725636129	NA	1.70E-35	mr1932	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
vg0725636129	NA	1.90E-18	mr1383_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
vg0725636129	NA	1.27E-21	mr1698_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
vg0725636129	NA	6.74E-18	mr1730_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
vg0725636129	NA	1.27E-20	mr1817_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
vg0725636129	5.69E-07	1.11E-07	mr1842_2	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
vg0725636129	NA	4.21E-15	mr1866_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