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Detailed information for vg0719999922:

Variant ID: vg0719999922 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 19999922
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGCTCCCCGACTTCTCCCCCCGGCCCCGACCCTGCAGAGATGGTCGGGTGAAAACCATCACTCGTCCTCGCCCCCGCAGGGGACCCGCGGGCGGGTGAGC[A/G]
GGGCCCCGCACCACCCGACTGAGGATTGACGAGCGAGGAGCCGAGGAGCAGGCGAGCAGCGATGACGCCGACAGGAACAACGAGGCTGGGGACTGGGCGT

Reverse complement sequence

ACGCCCAGTCCCCAGCCTCGTTGTTCCTGTCGGCGTCATCGCTGCTCGCCTGCTCCTCGGCTCCTCGCTCGTCAATCCTCAGTCGGGTGGTGCGGGGCCC[T/C]
GCTCACCCGCCCGCGGGTCCCCTGCGGGGGCGAGGACGAGTGATGGTTTTCACCCGACCATCTCTGCAGGGTCGGGGCCGGGGGGAGAAGTCGGGGAGCG

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	76.30%	23.60%	0.08%	0.00%	NA
All Indica	2759	89.80%	10.20%	0.04%	0.00%	NA
All Japonica	1512	69.80%	30.00%	0.13%	0.00%	NA
Aus	269	3.70%	96.30%	0.00%	0.00%	NA
Indica I	595	90.60%	9.20%	0.17%	0.00%	NA
Indica II	465	87.30%	12.70%	0.00%	0.00%	NA
Indica III	913	96.10%	3.90%	0.00%	0.00%	NA
Indica Intermediate	786	83.30%	16.70%	0.00%	0.00%	NA
Temperate Japonica	767	95.40%	4.60%	0.00%	0.00%	NA
Tropical Japonica	504	32.50%	67.30%	0.20%	0.00%	NA
Japonica Intermediate	241	66.40%	33.20%	0.41%	0.00%	NA
VI/Aromatic	96	8.30%	91.70%	0.00%	0.00%	NA
Intermediate	90	61.10%	37.80%	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
vg0719999922	A -> G	LOC_Os07g33460.1	upstream_gene_variant ; 62.0bp to feature; MODIFIER	silent_mutation	Average:76.927; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0719999922	A -> G	LOC_Os07g33470.1	upstream_gene_variant ; 3557.0bp to feature; MODIFIER	silent_mutation	Average:76.927; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0719999922	A -> G	LOC_Os07g33450.1	downstream_gene_variant ; 3566.0bp to feature; MODIFIER	silent_mutation	Average:76.927; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N
vg0719999922	A -> G	LOC_Os07g33450-LOC_Os07g33460	intergenic_region ; MODIFIER	silent_mutation	Average:76.927; most accessible tissue: Zhenshan97 young leaf, score: 84.035	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)
vg0719999922	A	G	0.03	0.03	0.02	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0719999922	NA	3.99E-07	mr1295	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
vg0719999922	NA	8.57E-06	mr1554	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
vg0719999922	2.82E-06	2.82E-06	mr1601	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
vg0719999922	NA	3.02E-06	mr1602	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
vg0719999922	NA	1.09E-08	mr1679	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
vg0719999922	NA	5.14E-07	mr1295_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
vg0719999922	NA	7.67E-06	mr1554_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