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Detailed information for vg0623064422:

Variant ID: vg0623064422 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23064422
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTAATTTCAGACAATATTATAATTTATTTTTCTTCTATCCGTGGCGGACCCAAGATTGGTTCAAGGCCCGAGCCAGCCCATATGGAGATTTAGGCCTTAT[T/G]
TGTTGTTTACATGGTGAAAAAATTATCATCTTAATGGACCTTCACACCTAGACCTTGGATCACGGCCCAGGTGGCCCAAGGCCTAGGTCCATCCCAGTCT

Reverse complement sequence

AGACTGGGATGGACCTAGGCCTTGGGCCACCTGGGCCGTGATCCAAGGTCTAGGTGTGAAGGTCCATTAAGATGATAATTTTTTCACCATGTAAACAACA[A/C]
ATAAGGCCTAAATCTCCATATGGGCTGGCTCGGGCCTTGAACCAATCTTGGGTCCGCCACGGATAGAAGAAAAATAAATTATAATATTGTCTGAAATTAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	68.10%	10.60%	6.43%	14.83%	NA
All Indica	2759	64.50%	14.50%	8.23%	12.79%	NA
All Japonica	1512	83.70%	2.20%	0.66%	13.49%	NA
Aus	269	27.10%	12.30%	24.16%	36.43%	NA
Indica I	595	79.30%	0.70%	6.72%	13.28%	NA
Indica II	465	72.90%	10.80%	7.53%	8.82%	NA
Indica III	913	49.50%	25.40%	10.84%	14.24%	NA
Indica Intermediate	786	65.80%	14.40%	6.74%	13.10%	NA
Temperate Japonica	767	81.20%	3.50%	0.39%	14.86%	NA
Tropical Japonica	504	88.30%	0.60%	0.60%	10.52%	NA
Japonica Intermediate	241	81.70%	1.20%	1.66%	15.35%	NA
VI/Aromatic	96	33.30%	30.20%	1.04%	35.42%	NA
Intermediate	90	75.60%	10.00%	1.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0623064422	T -> G	LOC_Os06g38870.1	upstream_gene_variant ; 2187.0bp to feature; MODIFIER	silent_mutation	Average:90.832; most accessible tissue: Zhenshan97 young leaf, score: 97.498	N	N	N	N
vg0623064422	T -> G	LOC_Os06g38850-LOC_Os06g38870	intergenic_region ; MODIFIER	silent_mutation	Average:90.832; most accessible tissue: Zhenshan97 young leaf, score: 97.498	N	N	N	N
vg0623064422	T -> DEL	N	N	silent_mutation	Average:90.832; most accessible tissue: Zhenshan97 young leaf, score: 97.498	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)
vg0623064422	T	G	0.16	0.17	0.11	0.17	0.15	0.15

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623064422	NA	4.29E-06	mr1057	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
vg0623064422	1.56E-08	9.32E-11	mr1057_2	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