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Detailed information for vg1125854393:

Variant ID: vg1125854393 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25854393
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.17, others allele: 0.00, population size: 41. )

Flanking Sequence (100 bp) in Reference Genome:

TGGGGGAGTTTTAGATTCTGAGAAGCGGCTTTTTGGTAGCCAGCTTCTGAGAATCTGGAAAAGCTCTTAAACCCAGCTTCTGGCTTCTTAATTCATTTTT[C/T]
AGAATCTGTAACTACAGATTCTCAGAAACTGTGGAATGTTTGGGGCAGCTTCTAACAGAAGCAGCTTTTGGGAAAAGCTGCAGCCGGGATAAGCTCCCTC

Reverse complement sequence

GAGGGAGCTTATCCCGGCTGCAGCTTTTCCCAAAAGCTGCTTCTGTTAGAAGCTGCCCCAAACATTCCACAGTTTCTGAGAATCTGTAGTTACAGATTCT[G/A]
AAAAATGAATTAAGAAGCCAGAAGCTGGGTTTAAGAGCTTTTCCAGATTCTCAGAAGCTGGCTACCAAAAAGCCGCTTCTCAGAATCTAAAACTCCCCCA

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	33.20%	29.30%	24.06%	13.42%	NA
All Indica	2759	48.00%	22.10%	22.91%	7.00%	NA
All Japonica	1512	8.90%	42.20%	24.01%	24.93%	NA
Aus	269	27.50%	23.40%	37.92%	11.15%	NA
Indica I	595	49.60%	46.40%	3.36%	0.67%	NA
Indica II	465	32.90%	9.20%	36.34%	21.51%	NA
Indica III	913	50.10%	17.10%	30.89%	1.97%	NA
Indica Intermediate	786	53.20%	17.30%	20.48%	9.03%	NA
Temperate Japonica	767	4.40%	64.70%	9.52%	21.38%	NA
Tropical Japonica	504	15.70%	8.10%	43.06%	33.13%	NA
Japonica Intermediate	241	8.70%	41.90%	30.29%	19.09%	NA
VI/Aromatic	96	3.10%	50.00%	27.08%	19.79%	NA
Intermediate	90	38.90%	28.90%	15.56%	16.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125854393	C -> T	LOC_Os11g42910.1	upstream_gene_variant ; 4486.0bp to feature; MODIFIER	silent_mutation	Average:56.658; most accessible tissue: Minghui63 panicle, score: 91.919	N	N	N	N
vg1125854393	C -> T	LOC_Os11g42900-LOC_Os11g42910	intergenic_region ; MODIFIER	silent_mutation	Average:56.658; most accessible tissue: Minghui63 panicle, score: 91.919	N	N	N	N
vg1125854393	C -> DEL	N	N	silent_mutation	Average:56.658; most accessible tissue: Minghui63 panicle, score: 91.919	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)
vg1125854393	C	T	0.02	-0.01	-0.01	0.01	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125854393	8.60E-07	8.60E-07	mr1068	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
vg1125854393	8.04E-12	9.10E-19	mr1191	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
vg1125854393	2.71E-08	1.59E-11	mr1191	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
vg1125854393	6.21E-06	6.21E-06	mr1609	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
vg1125854393	8.99E-17	6.99E-27	mr1644	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
vg1125854393	5.14E-10	4.79E-16	mr1644	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
vg1125854393	2.25E-06	2.25E-06	mr1644	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
vg1125854393	1.11E-13	8.53E-29	mr1191_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
vg1125854393	1.20E-09	1.14E-16	mr1191_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
vg1125854393	3.45E-06	3.45E-06	mr1191_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