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Detailed information for vg0430485059:

Variant ID: vg0430485059 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30485059
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGCTATTAGCCAGCTCTAAACATATTTTAATGAGATAAACGATGAGAGAGAAGAGCAGCGGGCTACAGATCTGTAGCCAGCTGCAGCACAGACTCCAAGA[T/C]
ACACTGTGTGTATGACATGTGGGACCATATATTAATAGTATAGCAAGCAACTATTATATGAATTGACTATTTGATTAGCTATAGATGAATTGGAGCTAGT

Reverse complement sequence

ACTAGCTCCAATTCATCTATAGCTAATCAAATAGTCAATTCATATAATAGTTGCTTGCTATACTATTAATATATGGTCCCACATGTCATACACACAGTGT[A/G]
TCTTGGAGTCTGTGCTGCAGCTGGCTACAGATCTGTAGCCCGCTGCTCTTCTCTCTCATCGTTTATCTCATTAAAATATGTTTAGAGCTGGCTAATAGCT

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	85.10%	14.90%	0.02%	0.00%	NA
All Indica	2759	98.00%	2.00%	0.00%	0.00%	NA
All Japonica	1512	58.90%	41.10%	0.07%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	96.60%	3.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	1.10%	0.00%	0.00%	NA
Temperate Japonica	767	38.90%	61.00%	0.13%	0.00%	NA
Tropical Japonica	504	84.70%	15.30%	0.00%	0.00%	NA
Japonica Intermediate	241	68.50%	31.50%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg0430485059	T -> C	LOC_Os04g51460.1	upstream_gene_variant ; 1567.0bp to feature; MODIFIER	silent_mutation	Average:95.678; most accessible tissue: Minghui63 flower, score: 97.811	N	N	N	N
vg0430485059	T -> C	LOC_Os04g51470.1	upstream_gene_variant ; 2060.0bp to feature; MODIFIER	silent_mutation	Average:95.678; most accessible tissue: Minghui63 flower, score: 97.811	N	N	N	N
vg0430485059	T -> C	LOC_Os04g51460-LOC_Os04g51470	intergenic_region ; MODIFIER	silent_mutation	Average:95.678; most accessible tissue: Minghui63 flower, score: 97.811	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)
vg0430485059	T	C	-0.01	-0.02	-0.01	-0.01	-0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430485059	NA	5.39E-08	mr1082	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
vg0430485059	NA	5.67E-06	mr1103	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
vg0430485059	NA	2.10E-07	mr1145	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
vg0430485059	NA	1.89E-09	mr1011_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
vg0430485059	8.82E-06	NA	mr1011_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
vg0430485059	NA	4.97E-08	mr1155_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
vg0430485059	NA	2.94E-08	mr1241_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