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Detailed information for vg0327431037:

Variant ID: vg0327431037 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 27431037
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.05, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCACTTAATTTCAAGGTCAGCATGTGGCCATGGGCTCCATTGATTCTTCTACTCCTACCTTGTCAACATGAGATTGAGACTTGACTTGAGAGAGTGTG[T/C]
AAAGTGACGACATGAACCCCCAAAAAAAAAACAACAACAAAAAAAAAACTGTAGTTGAAACAGAGAGGAAAGAGTGTGGACTGAAATGGACAGAAGGCCA

Reverse complement sequence

TGGCCTTCTGTCCATTTCAGTCCACACTCTTTCCTCTCTGTTTCAACTACAGTTTTTTTTTTGTTGTTGTTTTTTTTTTGGGGGTTCATGTCGTCACTTT[A/G]
CACACTCTCTCAAGTCAAGTCTCAATCTCATGTTGACAAGGTAGGAGTAGAAGAATCAATGGAGCCCATGGCCACATGCTGACCTTGAAATTAAGTGGAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.70%	46.10%	0.08%	0.11%	NA
All Indica	2759	22.30%	77.50%	0.14%	0.07%	NA
All Japonica	1512	99.20%	0.60%	0.00%	0.20%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	1.50%	98.50%	0.00%	0.00%	NA
Indica II	465	58.70%	40.90%	0.22%	0.22%	NA
Indica III	913	12.50%	87.30%	0.11%	0.11%	NA
Indica Intermediate	786	27.70%	72.00%	0.25%	0.00%	NA
Temperate Japonica	767	99.30%	0.40%	0.00%	0.26%	NA
Tropical Japonica	504	99.20%	0.60%	0.00%	0.20%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	70.00%	30.00%	0.00%	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
vg0327431037	T -> C	LOC_Os03g48190.2	downstream_gene_variant ; 787.0bp to feature; MODIFIER	silent_mutation	Average:94.87; most accessible tissue: Minghui63 flower, score: 98.948	N	N	N	N
vg0327431037	T -> C	LOC_Os03g48190.1	downstream_gene_variant ; 807.0bp to feature; MODIFIER	silent_mutation	Average:94.87; most accessible tissue: Minghui63 flower, score: 98.948	N	N	N	N
vg0327431037	T -> C	LOC_Os03g48180-LOC_Os03g48190	intergenic_region ; MODIFIER	silent_mutation	Average:94.87; most accessible tissue: Minghui63 flower, score: 98.948	N	N	N	N
vg0327431037	T -> DEL	N	N	silent_mutation	Average:94.87; most accessible tissue: Minghui63 flower, score: 98.948	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)
vg0327431037	T	C	0.0	0.07	0.01	-0.02	0.0	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0327431037	NA	1.61E-09	mr1193	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
vg0327431037	NA	1.76E-08	mr1557	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
vg0327431037	NA	1.12E-25	mr1598	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
vg0327431037	NA	7.56E-08	mr1598	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
vg0327431037	NA	2.76E-06	mr1679	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
vg0327431037	NA	5.38E-06	mr1693	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
vg0327431037	NA	4.69E-07	mr1717	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
vg0327431037	NA	1.48E-08	mr1860	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
vg0327431037	8.81E-09	NA	mr1193_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
vg0327431037	2.72E-07	4.52E-09	mr1193_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
vg0327431037	NA	1.10E-14	mr1514_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
vg0327431037	NA	9.25E-37	mr1598_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
vg0327431037	NA	1.63E-06	mr1754_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