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Detailed information for vg0122995888:

Variant ID: vg0122995888 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22995888
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAATCAACTTAAAATTAAAATTTAAATTTTAAATTTTGGTTAGGGCTTATAAGTTAGGCACAACAATCAATACCCTTATTGATAGACGTTGGTTGAAC[T/A]
TTTTTTTTTTTTTGGTGCTACGGTAGAATGACCCTTACCAAAGTTGGGTGGCATTTTCCTTTCTTTTTTTTCCCTACCCTTTTCGGCTTTGATGGCCAAG

Reverse complement sequence

CTTGGCCATCAAAGCCGAAAAGGGTAGGGAAAAAAAAGAAAGGAAAATGCCACCCAACTTTGGTAAGGGTCATTCTACCGTAGCACCAAAAAAAAAAAAA[A/T]
GTTCAACCAACGTCTATCAATAAGGGTATTGATTGTTGTGCCTAACTTATAAGCCCTAACCAAAATTTAAAATTTAAATTTTAATTTTAAGTTGATTTTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	45.60%	44.60%	5.56%	4.21%	NA
All Indica	2759	62.80%	33.80%	2.03%	1.38%	NA
All Japonica	1512	9.30%	67.50%	12.96%	10.32%	NA
Aus	269	92.60%	5.20%	2.23%	0.00%	NA
Indica I	595	48.60%	49.60%	1.18%	0.67%	NA
Indica II	465	44.50%	53.30%	1.08%	1.08%	NA
Indica III	913	82.80%	13.00%	1.86%	2.30%	NA
Indica Intermediate	786	61.10%	34.50%	3.44%	1.02%	NA
Temperate Japonica	767	12.90%	84.60%	1.17%	1.30%	NA
Tropical Japonica	504	0.80%	47.40%	29.17%	22.62%	NA
Japonica Intermediate	241	15.40%	54.80%	16.60%	13.28%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	32.20%	56.70%	5.56%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0122995888	T -> A	LOC_Os01g40680.1	upstream_gene_variant ; 1717.0bp to feature; MODIFIER	silent_mutation	Average:73.093; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0122995888	T -> A	LOC_Os01g40700.1	upstream_gene_variant ; 4103.0bp to feature; MODIFIER	silent_mutation	Average:73.093; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0122995888	T -> A	LOC_Os01g40670.1	downstream_gene_variant ; 3420.0bp to feature; MODIFIER	silent_mutation	Average:73.093; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0122995888	T -> A	LOC_Os01g40690.1	downstream_gene_variant ; 142.0bp to feature; MODIFIER	silent_mutation	Average:73.093; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0122995888	T -> A	LOC_Os01g40670.2	downstream_gene_variant ; 3420.0bp to feature; MODIFIER	silent_mutation	Average:73.093; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0122995888	T -> A	LOC_Os01g40690.2	downstream_gene_variant ; 142.0bp to feature; MODIFIER	silent_mutation	Average:73.093; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0122995888	T -> A	LOC_Os01g40680-LOC_Os01g40690	intergenic_region ; MODIFIER	silent_mutation	Average:73.093; most accessible tissue: Zhenshan97 flower, score: 87.73	N	N	N	N
vg0122995888	T -> DEL	N	N	silent_mutation	Average:73.093; most accessible tissue: Zhenshan97 flower, score: 87.73	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)
vg0122995888	T	A	0.02	0.0	-0.01	-0.01	-0.01	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122995888	NA	3.83E-28	mr1024	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
vg0122995888	2.97E-06	2.97E-06	mr1024	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
vg0122995888	NA	4.22E-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
vg0122995888	NA	3.02E-25	mr1024_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
vg0122995888	NA	3.25E-14	mr1333_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
vg0122995888	NA	1.58E-15	mr1686_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
vg0122995888	NA	1.23E-10	mr1806_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