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Detailed information for vg0235126397:

Variant ID: vg0235126397 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 35126397
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGACAAAGAAGCAGACAGAAAAACGTACAGAAAGCACCGTATCTGAAGGCGGCACTGCAACATCTCAGCAAACCAAAGGCCTACTAGTTGGCCAGGTA[C/T]
CAAGGGACTGACTTACTGGCAATTTCAGTCAAATAAGCCGTTTTTCATCAGAAGGATCCATGATACGGATTACGGAGTACTAACATATCACCATTTGTCG

Reverse complement sequence

CGACAAATGGTGATATGTTAGTACTCCGTAATCCGTATCATGGATCCTTCTGATGAAAAACGGCTTATTTGACTGAAATTGCCAGTAAGTCAGTCCCTTG[G/A]
TACCTGGCCAACTAGTAGGCCTTTGGTTTGCTGAGATGTTGCAGTGCCGCCTTCAGATACGGTGCTTTCTGTACGTTTTTCTGTCTGCTTCTTTGTCACT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.90%	32.70%	0.11%	0.34%	NA
All Indica	2759	88.50%	10.80%	0.14%	0.54%	NA
All Japonica	1512	26.60%	73.30%	0.00%	0.07%	NA
Aus	269	65.40%	34.60%	0.00%	0.00%	NA
Indica I	595	96.60%	2.90%	0.17%	0.34%	NA
Indica II	465	98.70%	1.10%	0.00%	0.22%	NA
Indica III	913	83.10%	16.20%	0.11%	0.55%	NA
Indica Intermediate	786	82.40%	16.40%	0.25%	0.89%	NA
Temperate Japonica	767	9.30%	90.70%	0.00%	0.00%	NA
Tropical Japonica	504	43.50%	56.50%	0.00%	0.00%	NA
Japonica Intermediate	241	46.50%	53.10%	0.00%	0.41%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	58.90%	40.00%	1.11%	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
vg0235126397	C -> T	LOC_Os02g57340.1	3_prime_UTR_variant ; 1753.0bp to feature; MODIFIER	silent_mutation	Average:77.022; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N
vg0235126397	C -> T	LOC_Os02g57330.1	upstream_gene_variant ; 3652.0bp to feature; MODIFIER	silent_mutation	Average:77.022; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N
vg0235126397	C -> T	LOC_Os02g57350.1	upstream_gene_variant ; 4277.0bp to feature; MODIFIER	silent_mutation	Average:77.022; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N
vg0235126397	C -> T	LOC_Os02g57330.2	upstream_gene_variant ; 3652.0bp to feature; MODIFIER	silent_mutation	Average:77.022; most accessible tissue: Minghui63 flower, score: 85.573	N	N	N	N
vg0235126397	C -> DEL	N	N	silent_mutation	Average:77.022; most accessible tissue: Minghui63 flower, score: 85.573	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)
vg0235126397	C	T	-0.03	-0.03	-0.03	-0.08	-0.04	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0235126397	NA	8.92E-07	mr1015	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
vg0235126397	NA	8.58E-06	mr1229	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
vg0235126397	6.00E-06	6.00E-06	mr1275	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
vg0235126397	8.46E-06	8.45E-06	mr1370	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
vg0235126397	3.50E-06	3.50E-06	mr1393	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
vg0235126397	NA	4.30E-06	mr1427	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
vg0235126397	NA	3.47E-06	mr1509	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
vg0235126397	NA	4.12E-06	mr1515	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
vg0235126397	5.29E-07	NA	mr1558	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
vg0235126397	6.07E-06	6.94E-08	mr1574	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
vg0235126397	NA	2.32E-06	mr1765	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
vg0235126397	NA	9.19E-09	mr1770	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
vg0235126397	NA	1.07E-07	mr1915	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
vg0235126397	NA	4.61E-07	mr1982	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