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Detailed information for vg0101342348:

Variant ID: vg0101342348 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 1342348
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

GTGAAATGCATGCATGGGGTGTTATTTATCGAGCAACTAAACTGAGAGCTAGCTATAAGAGCAAGTTTAATAGTATAGTCAACTATTAGCTCCAATTTAT[C/T]
TATAGCCAATCTGATAGCTCATTTATACAATAGTTACATACTACACTATCAATAACTAGTCCCACCTGTCATATATACACCGCGTCTTGGAGTCCGTACT

Reverse complement sequence

AGTACGGACTCCAAGACGCGGTGTATATATGACAGGTGGGACTAGTTATTGATAGTGTAGTATGTAACTATTGTATAAATGAGCTATCAGATTGGCTATA[G/A]
ATAAATTGGAGCTAATAGTTGACTATACTATTAAACTTGCTCTTATAGCTAGCTCTCAGTTTAGTTGCTCGATAAATAACACCCCATGCATGCATTTCAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.20%	17.50%	0.63%	7.70%	NA
All Indica	2759	70.40%	26.30%	0.69%	2.65%	NA
All Japonica	1512	91.00%	6.30%	0.07%	2.65%	NA
Aus	269	14.10%	0.00%	2.97%	82.90%	NA
Indica I	595	70.90%	28.10%	1.01%	0.00%	NA
Indica II	465	94.40%	5.20%	0.22%	0.22%	NA
Indica III	913	60.80%	35.80%	0.44%	2.96%	NA
Indica Intermediate	786	66.90%	26.30%	1.02%	5.73%	NA
Temperate Japonica	767	87.50%	12.00%	0.13%	0.39%	NA
Tropical Japonica	504	98.60%	0.40%	0.00%	0.99%	NA
Japonica Intermediate	241	86.30%	0.40%	0.00%	13.28%	NA
VI/Aromatic	96	80.20%	1.00%	1.04%	17.71%	NA
Intermediate	90	80.00%	6.70%	1.11%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0101342348	C -> T	LOC_Os01g03310.1	upstream_gene_variant ; 3209.0bp to feature; MODIFIER	silent_mutation	Average:87.257; most accessible tissue: Minghui63 young leaf, score: 97.127	N	N	N	N
vg0101342348	C -> T	LOC_Os01g03320.1	upstream_gene_variant ; 71.0bp to feature; MODIFIER	silent_mutation	Average:87.257; most accessible tissue: Minghui63 young leaf, score: 97.127	N	N	N	N
vg0101342348	C -> T	LOC_Os01g03300.1	downstream_gene_variant ; 4941.0bp to feature; MODIFIER	silent_mutation	Average:87.257; most accessible tissue: Minghui63 young leaf, score: 97.127	N	N	N	N
vg0101342348	C -> T	LOC_Os01g03330.1	downstream_gene_variant ; 2209.0bp to feature; MODIFIER	silent_mutation	Average:87.257; most accessible tissue: Minghui63 young leaf, score: 97.127	N	N	N	N
vg0101342348	C -> T	LOC_Os01g03320-LOC_Os01g03330	intergenic_region ; MODIFIER	silent_mutation	Average:87.257; most accessible tissue: Minghui63 young leaf, score: 97.127	N	N	N	N
vg0101342348	C -> DEL	N	N	silent_mutation	Average:87.257; most accessible tissue: Minghui63 young leaf, score: 97.127	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)
vg0101342348	C	T	0.07	0.04	0.01	-0.01	0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0101342348	NA	1.25E-06	mr1585	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
vg0101342348	NA	3.34E-06	mr1667	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
vg0101342348	NA	1.69E-09	mr1707	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
vg0101342348	NA	5.02E-06	mr1707	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
vg0101342348	NA	9.99E-11	mr1728	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
vg0101342348	NA	1.17E-07	mr1728	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
vg0101342348	NA	2.44E-06	mr1798	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
vg0101342348	NA	9.80E-06	mr1860	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
vg0101342348	2.83E-06	2.83E-06	mr1899	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
vg0101342348	NA	2.37E-06	mr1860_2	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