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Detailed information for vg1127574591:

Variant ID: vg1127574591 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27574591
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.18, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTCCACCATCATGGCTGTGACCATAGATAGTTTCACCATAACCGTGGAACCCCGTGTGTTTTGGTTTCATTTTGCTTTTCTTACTCCGAAAGCCTATA[C/T]
AATATGTGTCCTTTTCTGGATAAGGTGTTGGATTTTTTTTCCGCTGTTGTTAGTACTCTTTTCAAAATATTAAAACGGTGTGTTTCGTGTAAAAAAACTT

Reverse complement sequence

AAGTTTTTTTACACGAAACACACCGTTTTAATATTTTGAAAAGAGTACTAACAACAGCGGAAAAAAAATCCAACACCTTATCCAGAAAAGGACACATATT[G/A]
TATAGGCTTTCGGAGTAAGAAAAGCAAAATGAAACCAAAACACACGGGGTTCCACGGTTATGGTGAAACTATCTATGGTCACAGCCATGATGGTGGAGAC

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	58.10%	37.20%	0.21%	4.40%	NA
All Indica	2759	54.90%	41.20%	0.25%	3.59%	NA
All Japonica	1512	62.40%	30.20%	0.20%	7.21%	NA
Aus	269	62.10%	37.90%	0.00%	0.00%	NA
Indica I	595	86.10%	11.10%	0.00%	2.86%	NA
Indica II	465	84.50%	14.60%	0.65%	0.22%	NA
Indica III	913	18.30%	76.80%	0.11%	4.82%	NA
Indica Intermediate	786	56.40%	38.50%	0.38%	4.71%	NA
Temperate Japonica	767	76.40%	9.30%	0.26%	14.08%	NA
Tropical Japonica	504	38.70%	61.10%	0.20%	0.00%	NA
Japonica Intermediate	241	67.60%	32.00%	0.00%	0.41%	NA
VI/Aromatic	96	64.60%	35.40%	0.00%	0.00%	NA
Intermediate	90	66.70%	33.30%	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
vg1127574591	C -> T	LOC_Os11g45540.1	upstream_gene_variant ; 478.0bp to feature; MODIFIER	silent_mutation	Average:59.47; most accessible tissue: Minghui63 young leaf, score: 93.26	N	N	N	N
vg1127574591	C -> T	LOC_Os11g45550.1	downstream_gene_variant ; 448.0bp to feature; MODIFIER	silent_mutation	Average:59.47; most accessible tissue: Minghui63 young leaf, score: 93.26	N	N	N	N
vg1127574591	C -> T	LOC_Os11g45560.1	downstream_gene_variant ; 2085.0bp to feature; MODIFIER	silent_mutation	Average:59.47; most accessible tissue: Minghui63 young leaf, score: 93.26	N	N	N	N
vg1127574591	C -> T	LOC_Os11g45540-LOC_Os11g45550	intergenic_region ; MODIFIER	silent_mutation	Average:59.47; most accessible tissue: Minghui63 young leaf, score: 93.26	N	N	N	N
vg1127574591	C -> DEL	N	N	silent_mutation	Average:59.47; most accessible tissue: Minghui63 young leaf, score: 93.26	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)
vg1127574591	C	T	0.03	0.02	-0.01	-0.01	0.0	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127574591	NA	4.74E-08	mr1063	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
vg1127574591	3.22E-07	NA	mr1133	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
vg1127574591	1.14E-07	4.12E-17	mr1133	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
vg1127574591	1.24E-08	NA	mr1540	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
vg1127574591	4.80E-07	4.80E-07	mr1540	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
vg1127574591	2.72E-06	5.69E-10	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
vg1127574591	6.64E-06	NA	mr1732	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
vg1127574591	3.55E-06	NA	mr1732	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
vg1127574591	6.80E-06	1.16E-06	mr1803	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
vg1127574591	NA	1.27E-06	mr1063_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
vg1127574591	NA	2.80E-10	mr1065_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
vg1127574591	NA	2.53E-06	mr1096_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
vg1127574591	NA	4.26E-07	mr1111_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
vg1127574591	3.94E-07	5.28E-16	mr1133_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
vg1127574591	NA	7.93E-07	mr1144_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
vg1127574591	8.75E-06	4.72E-10	mr1667_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