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Detailed information for vg0601362892:

Variant ID: vg0601362892 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1362892
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAATCTGGAGGCCCAGCACGGACGATTACCTGCGGCCCAAGAATGGGGAAGTGATTAGCCCATACTAATTGGGCCATGATGGGATTCTGACTAATTGGG[C/A]
CTGAACAGGATTTCGATTTCTCACGGCCCACAAACGGATTTCAGTTTACGTGTGCGGCCCATATTTGCAGATTGGTAGCGATCGGAAATTTTACAGATTG

Reverse complement sequence

CAATCTGTAAAATTTCCGATCGCTACCAATCTGCAAATATGGGCCGCACACGTAAACTGAAATCCGTTTGTGGGCCGTGAGAAATCGAAATCCTGTTCAG[G/T]
CCCAATTAGTCAGAATCCCATCATGGCCCAATTAGTATGGGCTAATCACTTCCCCATTCTTGGGCCGCAGGTAATCGTCCGTGCTGGGCCTCCAGATTAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.90%	8.90%	0.13%	0.00%	NA
All Indica	2759	92.40%	7.50%	0.14%	0.00%	NA
All Japonica	1512	89.00%	10.80%	0.13%	0.00%	NA
Aus	269	92.60%	7.40%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	90.50%	9.20%	0.22%	0.00%	NA
Indica III	913	88.40%	11.50%	0.11%	0.00%	NA
Indica Intermediate	786	92.60%	7.10%	0.25%	0.00%	NA
Temperate Japonica	767	96.30%	3.40%	0.26%	0.00%	NA
Tropical Japonica	504	81.90%	18.10%	0.00%	0.00%	NA
Japonica Intermediate	241	80.50%	19.50%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0601362892	C -> A	LOC_Os06g03530.1	upstream_gene_variant ; 107.0bp to feature; MODIFIER	silent_mutation	Average:99.431; most accessible tissue: Minghui63 panicle, score: 99.705	N	N	N	N
vg0601362892	C -> A	LOC_Os06g03514.2	downstream_gene_variant ; 3844.0bp to feature; MODIFIER	silent_mutation	Average:99.431; most accessible tissue: Minghui63 panicle, score: 99.705	N	N	N	N
vg0601362892	C -> A	LOC_Os06g03520.1	downstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:99.431; most accessible tissue: Minghui63 panicle, score: 99.705	N	N	N	N
vg0601362892	C -> A	LOC_Os06g03540.1	downstream_gene_variant ; 2014.0bp to feature; MODIFIER	silent_mutation	Average:99.431; most accessible tissue: Minghui63 panicle, score: 99.705	N	N	N	N
vg0601362892	C -> A	LOC_Os06g03514.1	downstream_gene_variant ; 3846.0bp to feature; MODIFIER	silent_mutation	Average:99.431; most accessible tissue: Minghui63 panicle, score: 99.705	N	N	N	N
vg0601362892	C -> A	LOC_Os06g03520-LOC_Os06g03530	intergenic_region ; MODIFIER	silent_mutation	Average:99.431; most accessible tissue: Minghui63 panicle, score: 99.705	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)
vg0601362892	C	A	-0.08	-0.18	-0.12	-0.13	-0.08	-0.11

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601362892	5.51E-07	NA	mr1695	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
vg0601362892	5.78E-06	7.73E-08	mr1252_2	Jap_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
vg0601362892	NA	3.07E-07	mr1617_2	Jap_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
vg0601362892	NA	8.69E-06	mr1695_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