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Detailed information for vg0909369883:

Variant ID: vg0909369883 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 9369883
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAGGATGAAGTATCCGGTGATCTTCCCCTCGTACTGCTCCGCCCTCCCGGCGATCGCCTCGCCGCCGCCGCCGCCGAACCCTCCTGCCATCTTCTCTCT[C/T]
TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTCTCTGAGTTTCAGAGACAGAGATTCAGAGTCACACTCTTCCTCCTCTCCTCCCCA

Reverse complement sequence

TGGGGAGGAGAGGAGGAAGAGTGTGACTCTGAATCTCTGTCTCTGAAACTCAGAGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA[G/A]
AGAGAGAAGATGGCAGGAGGGTTCGGCGGCGGCGGCGGCGAGGCGATCGCCGGGAGGGCGGAGCAGTACGAGGGGAAGATCACCGGATACTTCATCCTCG

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	75.60%	4.20%	8.40%	11.83%	NA
All Indica	2759	79.30%	6.90%	6.20%	7.58%	NA
All Japonica	1512	72.30%	0.20%	8.07%	19.44%	NA
Aus	269	50.90%	0.70%	35.69%	12.64%	NA
Indica I	595	80.80%	5.40%	5.71%	8.07%	NA
Indica II	465	71.00%	9.20%	11.61%	8.17%	NA
Indica III	913	84.30%	7.20%	2.19%	6.24%	NA
Indica Intermediate	786	77.20%	6.40%	8.02%	8.40%	NA
Temperate Japonica	767	78.10%	0.10%	7.04%	14.73%	NA
Tropical Japonica	504	70.80%	0.00%	9.72%	19.44%	NA
Japonica Intermediate	241	56.80%	0.80%	7.88%	34.44%	NA
VI/Aromatic	96	81.20%	0.00%	2.08%	16.67%	NA
Intermediate	90	83.30%	3.30%	6.67%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0909369883	C -> DEL	N	N	silent_mutation	Average:84.356; most accessible tissue: Zhenshan97 root, score: 95.529	N	N	N	N
vg0909369883	C -> T	LOC_Os09g15330.1	5_prime_UTR_variant ; 10.0bp to feature; MODIFIER	silent_mutation	Average:84.356; most accessible tissue: Zhenshan97 root, score: 95.529	N	N	N	N
vg0909369883	C -> T	LOC_Os09g15330.2	5_prime_UTR_variant ; 10.0bp to feature; MODIFIER	silent_mutation	Average:84.356; most accessible tissue: Zhenshan97 root, score: 95.529	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)
vg0909369883	C	T	-0.02	-0.03	-0.03	-0.02	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0909369883	3.80E-06	7.12E-07	mr1961	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