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Detailed information for vg0228580947:

Variant ID: vg0228580947 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 28580947
Reference Allele: T	Alternative Allele: C
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: 124. )

Flanking Sequence (100 bp) in Reference Genome:

GAGGAGTCATCCCAGCATAGCATCGTTGCCGCCTGGTTGAGGATGAGGAGTCACTCGGGGAGGAGGAGCTCGAGCTCACCAGCGACAACAAACGCGCATC[T/C]
GTCTTCGTTTCCGCCGCAACAGCGACGCCACGGCCCCTGTCCCTTCATCCCCGTGCTCGTCCCCACCCCTTCATCTCCCCATCTTCTCCAATCTTGGCCG

Reverse complement sequence

CGGCCAAGATTGGAGAAGATGGGGAGATGAAGGGGTGGGGACGAGCACGGGGATGAAGGGACAGGGGCCGTGGCGTCGCTGTTGCGGCGGAAACGAAGAC[A/G]
GATGCGCGTTTGTTGTCGCTGGTGAGCTCGAGCTCCTCCTCCCCGAGTGACTCCTCATCCTCAACCAGGCGGCAACGATGCTATGCTGGGATGACTCCTC

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	89.30%	10.30%	0.38%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.04%	0.00%	NA
All Japonica	1512	68.70%	30.20%	1.12%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.10%	0.90%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	1.30%	0.13%	0.00%	NA
Temperate Japonica	767	45.80%	52.40%	1.83%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	77.60%	21.20%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg0228580947	T -> C	LOC_Os02g46839.1	upstream_gene_variant ; 613.0bp to feature; MODIFIER	silent_mutation	Average:72.029; most accessible tissue: Minghui63 root, score: 84.323	N	N	N	N
vg0228580947	T -> C	LOC_Os02g46820.1	downstream_gene_variant ; 4190.0bp to feature; MODIFIER	silent_mutation	Average:72.029; most accessible tissue: Minghui63 root, score: 84.323	N	N	N	N
vg0228580947	T -> C	LOC_Os02g46830.1	downstream_gene_variant ; 1771.0bp to feature; MODIFIER	silent_mutation	Average:72.029; most accessible tissue: Minghui63 root, score: 84.323	N	N	N	N
vg0228580947	T -> C	LOC_Os02g46850.1	downstream_gene_variant ; 599.0bp to feature; MODIFIER	silent_mutation	Average:72.029; most accessible tissue: Minghui63 root, score: 84.323	N	N	N	N
vg0228580947	T -> C	LOC_Os02g46860.1	downstream_gene_variant ; 4356.0bp to feature; MODIFIER	silent_mutation	Average:72.029; most accessible tissue: Minghui63 root, score: 84.323	N	N	N	N
vg0228580947	T -> C	LOC_Os02g46830-LOC_Os02g46850	intergenic_region ; MODIFIER	silent_mutation	Average:72.029; most accessible tissue: Minghui63 root, score: 84.323	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)
vg0228580947	T	C	0.03	0.01	0.02	0.03	0.04	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0228580947	NA	8.19E-08	mr1069	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
vg0228580947	NA	3.79E-07	mr1617	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
vg0228580947	NA	2.29E-06	mr1627	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
vg0228580947	4.04E-06	1.30E-15	mr1712	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
vg0228580947	NA	3.05E-06	mr1712	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
vg0228580947	NA	1.08E-08	mr1748	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
vg0228580947	NA	9.85E-06	mr1748	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
vg0228580947	NA	6.92E-07	mr1910	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
vg0228580947	NA	2.60E-08	mr1977	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
vg0228580947	NA	9.54E-09	mr1627_2	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
vg0228580947	NA	3.02E-08	mr1748_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