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Detailed information for vg0433003871:

Variant ID: vg0433003871 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 33003871
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.07, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGTGGGTAACGACAGCGTCGCGTACTCCTCTCCTCTCCTCTCACATGTGTCCGGCAATGGCGGGGTTGACTCATGGCCATGGCGTCACGCGCCAATTT[C/A]
CCGGACGCGCGAGAGAGGGAGATAGAGAGAGGGCAAGTTGTCCTGGACAACCCACCCAGGCGCACGGCACGATGAGCTGTGAATTGTTGTGATTCCCAGT

Reverse complement sequence

ACTGGGAATCACAACAATTCACAGCTCATCGTGCCGTGCGCCTGGGTGGGTTGTCCAGGACAACTTGCCCTCTCTCTATCTCCCTCTCTCGCGCGTCCGG[G/T]
AAATTGGCGCGTGACGCCATGGCCATGAGTCAACCCCGCCATTGCCGGACACATGTGAGAGGAGAGGAGAGGAGTACGCGACGCTGTCGTTACCCACCAA

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	65.90%	34.10%	0.04%	0.00%	NA
All Indica	2759	95.70%	4.30%	0.00%	0.00%	NA
All Japonica	1512	14.00%	85.90%	0.07%	0.00%	NA
Aus	269	53.50%	46.50%	0.00%	0.00%	NA
Indica I	595	94.30%	5.70%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	94.60%	5.40%	0.00%	0.00%	NA
Indica Intermediate	786	96.40%	3.60%	0.00%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	37.90%	62.10%	0.00%	0.00%	NA
Japonica Intermediate	241	6.20%	93.40%	0.41%	0.00%	NA
VI/Aromatic	96	68.80%	30.20%	1.04%	0.00%	NA
Intermediate	90	58.90%	41.10%	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
vg0433003871	C -> A	LOC_Os04g55480.1	upstream_gene_variant ; 4089.0bp to feature; MODIFIER	silent_mutation	Average:90.078; most accessible tissue: Zhenshan97 panicle, score: 98.272	N	N	N	N
vg0433003871	C -> A	LOC_Os04g55500.1	upstream_gene_variant ; 2453.0bp to feature; MODIFIER	silent_mutation	Average:90.078; most accessible tissue: Zhenshan97 panicle, score: 98.272	N	N	N	N
vg0433003871	C -> A	LOC_Os04g55480.2	upstream_gene_variant ; 4089.0bp to feature; MODIFIER	silent_mutation	Average:90.078; most accessible tissue: Zhenshan97 panicle, score: 98.272	N	N	N	N
vg0433003871	C -> A	LOC_Os04g55490.1	downstream_gene_variant ; 864.0bp to feature; MODIFIER	silent_mutation	Average:90.078; most accessible tissue: Zhenshan97 panicle, score: 98.272	N	N	N	N
vg0433003871	C -> A	LOC_Os04g55490-LOC_Os04g55500	intergenic_region ; MODIFIER	silent_mutation	Average:90.078; most accessible tissue: Zhenshan97 panicle, score: 98.272	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)
vg0433003871	C	A	-0.29	-0.17	-0.09	0.07	-0.1	-0.11

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0433003871	NA	1.18E-08	mr1040	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
vg0433003871	NA	3.85E-06	mr1072_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
vg0433003871	NA	3.84E-06	mr1077_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
vg0433003871	NA	7.48E-08	mr1097_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
vg0433003871	3.88E-06	NA	mr1146_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
vg0433003871	NA	6.27E-07	mr1243_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
vg0433003871	NA	2.15E-06	mr1248_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
vg0433003871	NA	3.43E-06	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
vg0433003871	NA	6.33E-06	mr1253_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
vg0433003871	NA	6.46E-08	mr1295_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
vg0433003871	NA	1.07E-07	mr1498_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
vg0433003871	NA	3.42E-06	mr1567_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
vg0433003871	NA	2.92E-08	mr1800_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