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Detailed information for vg0821378221:

Variant ID: vg0821378221 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21378221
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCCTGGCTATTTTGCGAGACGAATCTAACAAGGTATATTAATTCATGATTTGCTACAGTGATGCTACAGTAATTATCCGCTAACCATAGATTAATATAC[C/A]
TCGTTAGATTCGTCTCGCAAAATAGTCCAGGGGTTATGGAATGAGTTTTGTCAGTAATTTATGTTTAATACTCCTAAATAGCAATATTTTATATAGCTAT

Reverse complement sequence

ATAGCTATATAAAATATTGCTATTTAGGAGTATTAAACATAAATTACTGACAAAACTCATTCCATAACCCCTGGACTATTTTGCGAGACGAATCTAACGA[G/T]
GTATATTAATCTATGGTTAGCGGATAATTACTGTAGCATCACTGTAGCAAATCATGAATTAATATACCTTGTTAGATTCGTCTCGCAAAATAGCCAGGGG

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	67.20%	22.20%	0.06%	10.54%	NA
All Indica	2759	98.60%	1.10%	0.00%	0.36%	NA
All Japonica	1512	5.40%	63.10%	0.20%	31.28%	NA
Aus	269	91.80%	8.20%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	97.20%	2.60%	0.00%	0.22%	NA
Indica III	913	99.60%	0.30%	0.00%	0.11%	NA
Indica Intermediate	786	97.30%	1.80%	0.00%	0.89%	NA
Temperate Japonica	767	1.00%	96.30%	0.00%	2.61%	NA
Tropical Japonica	504	10.10%	17.70%	0.60%	71.63%	NA
Japonica Intermediate	241	9.50%	52.30%	0.00%	38.17%	NA
VI/Aromatic	96	80.20%	19.80%	0.00%	0.00%	NA
Intermediate	90	54.40%	28.90%	0.00%	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
vg0821378221	C -> A	LOC_Os08g34090.1	upstream_gene_variant ; 3749.0bp to feature; MODIFIER	silent_mutation	Average:75.089; most accessible tissue: Zhenshan97 panicle, score: 93.936	N	N	N	N
vg0821378221	C -> A	LOC_Os08g34100.1	downstream_gene_variant ; 2978.0bp to feature; MODIFIER	silent_mutation	Average:75.089; most accessible tissue: Zhenshan97 panicle, score: 93.936	N	N	N	N
vg0821378221	C -> A	LOC_Os08g34090-LOC_Os08g34100	intergenic_region ; MODIFIER	silent_mutation	Average:75.089; most accessible tissue: Zhenshan97 panicle, score: 93.936	N	N	N	N
vg0821378221	C -> DEL	N	N	silent_mutation	Average:75.089; most accessible tissue: Zhenshan97 panicle, score: 93.936	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)
vg0821378221	C	A	0.0	0.0	0.0	-0.03	-0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821378221	NA	1.38E-56	mr1241	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
vg0821378221	NA	8.57E-21	mr1689	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
vg0821378221	NA	3.10E-08	mr1806	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
vg0821378221	NA	2.17E-21	mr1401_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
vg0821378221	NA	7.81E-10	mr1660_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
vg0821378221	NA	1.34E-73	mr1778_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