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Detailed information for vg1124001841:

Variant ID: vg1124001841 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24001841
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCGTTCTACTCCCGGGCATCACTCTCCTGGAGCTTCCGTTGCTCCGGCCGGCGCTATCATGCCACCGGGGTTTCCGACTTTCCCTCCCAGAAGGCTTT[C/A]
CCTCCCCGTCTCCGGCCAACTCTGGTCTCCGGCCATCTCCTCGTCGGCGGGGGCAACCTAGCAGTGGACTAGCGGAAGGATCGGAAGGCCACATTCCCAG

Reverse complement sequence

CTGGGAATGTGGCCTTCCGATCCTTCCGCTAGTCCACTGCTAGGTTGCCCCCGCCGACGAGGAGATGGCCGGAGACCAGAGTTGGCCGGAGACGGGGAGG[G/T]
AAAGCCTTCTGGGAGGGAAAGTCGGAAACCCCGGTGGCATGATAGCGCCGGCCGGAGCAACGGAAGCTCCAGGAGAGTGATGCCCGGGAGTAGAACGGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.60%	17.90%	0.23%	26.20%	NA
All Indica	2759	78.40%	2.90%	0.00%	18.70%	NA
All Japonica	1512	22.20%	41.40%	0.53%	35.85%	NA
Aus	269	18.60%	45.40%	0.00%	36.06%	NA
Indica I	595	77.50%	3.50%	0.00%	18.99%	NA
Indica II	465	92.00%	0.60%	0.00%	7.31%	NA
Indica III	913	72.30%	1.30%	0.00%	26.40%	NA
Indica Intermediate	786	78.20%	5.50%	0.00%	16.28%	NA
Temperate Japonica	767	13.40%	54.50%	0.39%	31.68%	NA
Tropical Japonica	504	19.80%	34.10%	0.79%	45.24%	NA
Japonica Intermediate	241	55.20%	14.90%	0.41%	29.46%	NA
VI/Aromatic	96	30.20%	2.10%	1.04%	66.67%	NA
Intermediate	90	56.70%	20.00%	2.22%	21.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1124001841	C -> A	LOC_Os11g40249.1	5_prime_UTR_variant ; 4600.0bp to feature; MODIFIER	silent_mutation	Average:59.404; most accessible tissue: Zhenshan97 panicle, score: 96.214	N	N	N	N
vg1124001841	C -> A	LOC_Os11g40249.3	5_prime_UTR_variant ; 4600.0bp to feature; MODIFIER	silent_mutation	Average:59.404; most accessible tissue: Zhenshan97 panicle, score: 96.214	N	N	N	N
vg1124001841	C -> A	LOC_Os11g40249.4	5_prime_UTR_variant ; 4600.0bp to feature; MODIFIER	silent_mutation	Average:59.404; most accessible tissue: Zhenshan97 panicle, score: 96.214	N	N	N	N
vg1124001841	C -> A	LOC_Os11g40249.2	5_prime_UTR_variant ; 4600.0bp to feature; MODIFIER	silent_mutation	Average:59.404; most accessible tissue: Zhenshan97 panicle, score: 96.214	N	N	N	N
vg1124001841	C -> A	LOC_Os11g40230.1	upstream_gene_variant ; 2484.0bp to feature; MODIFIER	silent_mutation	Average:59.404; most accessible tissue: Zhenshan97 panicle, score: 96.214	N	N	N	N
vg1124001841	C -> DEL	N	N	silent_mutation	Average:59.404; most accessible tissue: Zhenshan97 panicle, score: 96.214	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)
vg1124001841	C	A	-0.01	-0.01	-0.01	0.0	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124001841	6.28E-07	NA	mr1102_2	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
vg1124001841	3.20E-07	NA	mr1223_2	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
vg1124001841	NA	1.06E-10	mr1228_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
vg1124001841	NA	2.86E-07	mr1407_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
vg1124001841	NA	6.39E-06	mr1869_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