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Detailed information for vg0912185687:

Variant ID: vg0912185687 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 12185687
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.07, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

GGCAGTGCTCTGAAGCATAACTTCAGGCAATCAAAGAGGGGTGCTTGCTGGCTCTAATGGACCCTCTTCCCGATTGTAATAGAGACCGACTGTATGGTGG[T/C]
ACTGCATTTGATCCAGTCGAAGGAGAAGAATTTGTCGGAACTGGCTTTTCTAGTCAAGGAGATGAGTGACCTCTTGACTGGTAACAGGGAATTCTTGCTC

Reverse complement sequence

GAGCAAGAATTCCCTGTTACCAGTCAAGAGGTCACTCATCTCCTTGACTAGAAAAGCCAGTTCCGACAAATTCTTCTCCTTCGACTGGATCAAATGCAGT[A/G]
CCACCATACAGTCGGTCTCTATTACAATCGGGAAGAGGGTCCATTAGAGCCAGCAAGCACCCCTCTTTGATTGCCTGAAGTTATGCTTCAGAGCACTGCC

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	51.90%	47.40%	0.61%	0.00%	NA
All Indica	2759	26.60%	72.50%	0.87%	0.00%	NA
All Japonica	1512	99.00%	0.90%	0.13%	0.00%	NA
Aus	269	31.20%	68.80%	0.00%	0.00%	NA
Indica I	595	7.20%	91.90%	0.84%	0.00%	NA
Indica II	465	53.80%	45.40%	0.86%	0.00%	NA
Indica III	913	24.90%	74.60%	0.55%	0.00%	NA
Indica Intermediate	786	27.20%	71.50%	1.27%	0.00%	NA
Temperate Japonica	767	99.20%	0.70%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	77.10%	22.90%	0.00%	0.00%	NA
Intermediate	90	73.30%	23.30%	3.33%	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
vg0912185687	T -> C	LOC_Os09g20310.1	upstream_gene_variant ; 4014.0bp to feature; MODIFIER	silent_mutation	Average:69.035; most accessible tissue: Zhenshan97 root, score: 86.362	N	N	N	N
vg0912185687	T -> C	LOC_Os09g20300-LOC_Os09g20310	intergenic_region ; MODIFIER	silent_mutation	Average:69.035; most accessible tissue: Zhenshan97 root, score: 86.362	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)
vg0912185687	T	C	-0.1	-0.04	-0.03	-0.05	-0.07	-0.09

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0912185687	NA	2.23E-10	mr1425	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
vg0912185687	1.30E-06	4.79E-11	mr1425	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
vg0912185687	NA	4.31E-08	mr1660	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
vg0912185687	NA	3.37E-12	mr1667	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
vg0912185687	NA	1.09E-08	mr1986	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
vg0912185687	NA	8.93E-06	mr1497_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
vg0912185687	NA	1.27E-08	mr1660_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
vg0912185687	NA	3.65E-14	mr1717_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
vg0912185687	NA	1.12E-07	mr1895_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
vg0912185687	NA	3.29E-07	mr1895_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
vg0912185687	NA	4.78E-10	mr1946_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
vg0912185687	NA	4.78E-10	mr1948_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