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Detailed information for vg0602041810:

Variant ID: vg0602041810 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 2041810
Reference Allele: G	Alternative Allele: T,A
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTAACCAACAAATATATGACCATAACCATTGAATGAACTTGTTCAGAAGAGTTGTCTGCTACAGCGCTGTGGCTGCAACAACTGCTACAACGTCTAAC[G/T,A]
TACTCCCTCCGTCCCATAATATAAAGGATTTTCAGTTTTTTCTTGCAACGTTTGACCACTCGTCTTATTCATTTTTTTTTTGCAAATATAAAAAACGAAA

Reverse complement sequence

TTTCGTTTTTTATATTTGCAAAAAAAAAATGAATAAGACGAGTGGTCAAACGTTGCAAGAAAAAACTGAAAATCCTTTATATTATGGGACGGAGGGAGTA[C/A,T]
GTTAGACGTTGTAGCAGTTGTTGCAGCCACAGCGCTGTAGCAGACAACTCTTCTGAACAAGTTCATTCAATGGTTATGGTCATATATTTGTTGGTTAAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.00%	3.50%	0.49%	0.00%	A: 0.04%
All Indica	2759	97.80%	2.00%	0.18%	0.00%	A: 0.07%
All Japonica	1512	92.10%	6.70%	1.12%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	94.40%	4.70%	0.86%	0.00%	NA
Indica III	913	99.60%	0.20%	0.00%	0.00%	A: 0.22%
Indica Intermediate	786	96.10%	3.80%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	77.00%	19.80%	3.17%	0.00%	NA
Japonica Intermediate	241	98.80%	0.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0602041810	G -> T	LOC_Os06g04680.1	upstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> T	LOC_Os06g04680.2	upstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> T	LOC_Os06g04670.1	downstream_gene_variant ; 4032.0bp to feature; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> T	LOC_Os06g04690.1	downstream_gene_variant ; 1622.0bp to feature; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> T	LOC_Os06g04680-LOC_Os06g04690	intergenic_region ; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> A	LOC_Os06g04680.1	upstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> A	LOC_Os06g04680.2	upstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> A	LOC_Os06g04670.1	downstream_gene_variant ; 4032.0bp to feature; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> A	LOC_Os06g04690.1	downstream_gene_variant ; 1622.0bp to feature; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	N	N	N	N
vg0602041810	G -> A	LOC_Os06g04680-LOC_Os06g04690	intergenic_region ; MODIFIER	silent_mutation	Average:84.961; most accessible tissue: Callus, score: 97.829	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)
vg0602041810	G	A	-0.06	-0.05	-0.05	-0.04	-0.04	-0.03
vg0602041810	G	T	-0.01	0.01	0.03	-0.04	-0.02	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0602041810	NA	2.91E-06	mr1082	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
vg0602041810	5.13E-07	1.08E-09	mr1083	Jap_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
vg0602041810	NA	6.77E-07	mr1226	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
vg0602041810	2.11E-08	2.11E-08	mr1076_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
vg0602041810	NA	5.05E-07	mr1082_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
vg0602041810	NA	7.28E-08	mr1083_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
vg0602041810	2.36E-06	1.12E-07	mr1226_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
vg0602041810	NA	5.20E-06	mr1408_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