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Detailed information for vg0203590903:

Variant ID: vg0203590903 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 3590903
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTTTCGTCCACATTTAATGCTCTTTACATGTGTCCAAACATTTGATGTGACGGAAAAGTTGGAAGTTTAAAAAAAACTAAACACAGTCCACAAATACAG[A/G]
TAAGTCTGATTAAGAAAAAAATCAAAATGAGTTATAAAGGGAGGATTATTTAAAGCACATAATTTAAACCGACAGACATATTGCTGTAAAAGCGCGTGGT

Reverse complement sequence

ACCACGCGCTTTTACAGCAATATGTCTGTCGGTTTAAATTATGTGCTTTAAATAATCCTCCCTTTATAACTCATTTTGATTTTTTTCTTAATCAGACTTA[T/C]
CTGTATTTGTGGACTGTGTTTAGTTTTTTTTAAACTTCCAACTTTTCCGTCACATCAAATGTTTGGACACATGTAAAGAGCATTAAATGTGGACGAAAAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.40%	2.90%	0.66%	0.00%	NA
All Indica	2759	99.40%	0.30%	0.36%	0.00%	NA
All Japonica	1512	93.80%	5.00%	1.19%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.20%	0.00%	0.84%	0.00%	NA
Indica II	465	98.90%	0.60%	0.43%	0.00%	NA
Indica III	913	99.60%	0.30%	0.11%	0.00%	NA
Indica Intermediate	786	99.60%	0.10%	0.25%	0.00%	NA
Temperate Japonica	767	98.80%	0.30%	0.91%	0.00%	NA
Tropical Japonica	504	96.20%	3.60%	0.20%	0.00%	NA
Japonica Intermediate	241	73.00%	22.80%	4.15%	0.00%	NA
VI/Aromatic	96	50.00%	47.90%	2.08%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	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
vg0203590903	A -> G	LOC_Os02g07020.1	upstream_gene_variant ; 2869.0bp to feature; MODIFIER	silent_mutation	Average:55.775; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0203590903	A -> G	LOC_Os02g07030.1	upstream_gene_variant ; 3406.0bp to feature; MODIFIER	silent_mutation	Average:55.775; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0203590903	A -> G	LOC_Os02g07030.2	upstream_gene_variant ; 3326.0bp to feature; MODIFIER	silent_mutation	Average:55.775; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0203590903	A -> G	LOC_Os02g07030.3	upstream_gene_variant ; 3327.0bp to feature; MODIFIER	silent_mutation	Average:55.775; most accessible tissue: Zhenshan97 panicle, score: 82.336	N	N	N	N
vg0203590903	A -> G	LOC_Os02g07020-LOC_Os02g07030	intergenic_region ; MODIFIER	silent_mutation	Average:55.775; most accessible tissue: Zhenshan97 panicle, score: 82.336	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)
vg0203590903	A	G	0.03	0.01	0.0	0.02	0.03	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0203590903	NA	2.84E-06	mr1123	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
vg0203590903	NA	6.20E-07	mr1242	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
vg0203590903	NA	1.41E-08	mr1693	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
vg0203590903	NA	1.89E-07	mr1240_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
vg0203590903	NA	4.05E-07	mr1242_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
vg0203590903	NA	7.24E-08	mr1350_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
vg0203590903	NA	4.86E-07	mr1495_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
vg0203590903	NA	7.83E-07	mr1496_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
vg0203590903	NA	1.42E-06	mr1519_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
vg0203590903	NA	1.43E-06	mr1691_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
vg0203590903	NA	1.50E-08	mr1861_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
vg0203590903	2.40E-06	NA	mr1962_2	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