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Detailed information for vg0402290226:

Variant ID: vg0402290226 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2290226
Reference Allele: G	Alternative Allele: C,T
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, C: 0.04, others allele: 0.00, population size: 69. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGGCCCTCAGCTCCCCTCTCCCTCAGCCCCTCAGCGACCGTGGGCATTCCGGGGGCAGCGACGGCAAGGTGCGGGGTCGGCGGACAACGGCGAGGCGT[G/C,T]
AGGTCGGTGATGGCGAGGCATGGGGTGGGCGACGGCGATGCGCGGGGGCGGCGGCATCCACCCTCGGCGCGGCTCCTCTCCCCTCCCTTCTAGATGTGGC

Reverse complement sequence

GCCACATCTAGAAGGGAGGGGAGAGGAGCCGCGCCGAGGGTGGATGCCGCCGCCCCCGCGCATCGCCGTCGCCCACCCCATGCCTCGCCATCACCGACCT[C/G,A]
ACGCCTCGCCGTTGTCCGCCGACCCCGCACCTTGCCGTCGCTGCCCCCGGAATGCCCACGGTCGCTGAGGGGCTGAGGGAGAGGGGAGCTGAGGGCCGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.50%	35.20%	0.83%	11.34%	T: 0.15%
All Indica	2759	45.70%	52.10%	1.05%	0.91%	T: 0.25%
All Japonica	1512	60.40%	11.90%	0.26%	27.45%	NA
Aus	269	85.10%	1.10%	1.12%	12.64%	NA
Indica I	595	44.90%	54.50%	0.50%	0.17%	NA
Indica II	465	8.20%	90.80%	0.65%	0.43%	NA
Indica III	913	66.50%	31.10%	1.10%	1.10%	T: 0.22%
Indica Intermediate	786	44.40%	51.80%	1.65%	1.53%	T: 0.64%
Temperate Japonica	767	75.50%	0.70%	0.26%	23.60%	NA
Tropical Japonica	504	40.50%	32.10%	0.40%	26.98%	NA
Japonica Intermediate	241	53.90%	5.40%	0.00%	40.66%	NA
VI/Aromatic	96	43.80%	5.20%	2.08%	48.96%	NA
Intermediate	90	41.10%	41.10%	1.11%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0402290226	G -> C	LOC_Os04g04770.1	upstream_gene_variant ; 1794.0bp to feature; MODIFIER	silent_mutation	Average:74.143; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0402290226	G -> C	LOC_Os04g04780.1	downstream_gene_variant ; 3988.0bp to feature; MODIFIER	silent_mutation	Average:74.143; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0402290226	G -> C	LOC_Os04g04750-LOC_Os04g04770	intergenic_region ; MODIFIER	silent_mutation	Average:74.143; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0402290226	G -> DEL	N	N	silent_mutation	Average:74.143; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0402290226	G -> T	LOC_Os04g04770.1	upstream_gene_variant ; 1794.0bp to feature; MODIFIER	silent_mutation	Average:74.143; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0402290226	G -> T	LOC_Os04g04780.1	downstream_gene_variant ; 3988.0bp to feature; MODIFIER	silent_mutation	Average:74.143; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg0402290226	G -> T	LOC_Os04g04750-LOC_Os04g04770	intergenic_region ; MODIFIER	silent_mutation	Average:74.143; most accessible tissue: Zhenshan97 panicle, score: 86.058	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)
vg0402290226	G	C	0.0	0.0	0.0	0.0	0.0	0.0
vg0402290226	G	T	0.0	-0.01	-0.01	0.0	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402290226	NA	2.42E-09	mr1352	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
vg0402290226	NA	1.10E-06	mr1728	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
vg0402290226	1.29E-07	NA	mr1798	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
vg0402290226	1.30E-07	5.79E-10	mr1798	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
vg0402290226	3.71E-06	NA	mr1037_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
vg0402290226	NA	1.03E-06	mr1126_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
vg0402290226	NA	5.93E-09	mr1707_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
vg0402290226	1.31E-13	NA	mr1798_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
vg0402290226	6.59E-12	1.78E-16	mr1798_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