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Detailed information for vg0143143412:

Variant ID: vg0143143412 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 43143412
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTCCTTCCATGTCTCGCATGCATCCCCAGAGTAATCAGCGCGTTTTTTTTGCCTTCTGGCTATCAATTACAGTACATTTGTGTTTAAAAGACAGGCTAA[T/A]
CCCATACAGTCACAAGTCTTCTGTTCAGTAAAAAAAAAAGGTACAGTGATTGTTCTGTACAAATAAAAAAAGGATAAAGCAGAAAAAGAGAGGCGACCGC

Reverse complement sequence

GCGGTCGCCTCTCTTTTTCTGCTTTATCCTTTTTTTATTTGTACAGAACAATCACTGTACCTTTTTTTTTTACTGAACAGAAGACTTGTGACTGTATGGG[A/T]
TTAGCCTGTCTTTTAAACACAAATGTACTGTAATTGATAGCCAGAAGGCAAAAAAAACGCGCTGATTACTCTGGGGATGCATGCGAGACATGGAAGGAGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.90%	23.80%	2.41%	0.85%	NA
All Indica	2759	54.40%	40.10%	4.02%	1.41%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.07%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	49.60%	49.60%	0.84%	0.00%	NA
Indica II	465	69.50%	19.10%	7.96%	3.44%	NA
Indica III	913	46.30%	48.60%	4.16%	0.88%	NA
Indica Intermediate	786	58.70%	35.50%	3.94%	1.91%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	11.10%	2.22%	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
vg0143143412	T -> A	LOC_Os01g74500.1	upstream_gene_variant ; 305.0bp to feature; MODIFIER	silent_mutation	Average:97.187; most accessible tissue: Zhenshan97 root, score: 99.334	N	N	N	N
vg0143143412	T -> A	LOC_Os01g74490.1	downstream_gene_variant ; 742.0bp to feature; MODIFIER	silent_mutation	Average:97.187; most accessible tissue: Zhenshan97 root, score: 99.334	N	N	N	N
vg0143143412	T -> A	LOC_Os01g74490-LOC_Os01g74500	intergenic_region ; MODIFIER	silent_mutation	Average:97.187; most accessible tissue: Zhenshan97 root, score: 99.334	N	N	N	N
vg0143143412	T -> DEL	N	N	silent_mutation	Average:97.187; most accessible tissue: Zhenshan97 root, score: 99.334	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)
vg0143143412	T	A	-0.03	-0.04	-0.03	0.0	-0.02	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0143143412	NA	2.68E-06	mr1974	Ind_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
vg0143143412	1.07E-07	7.94E-06	mr1974_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
vg0143143412	3.29E-07	1.37E-09	mr1974_2	Ind_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