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Detailed information for vg0814414168:

Variant ID: vg0814414168 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 14414168
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.03, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

GCCATATCCATCAAAATATGTATGGACATATCCCATCCATGCATGACCGTGAACCAAACACACCCTTAAGTATCCTATCCTCTAGTCTCTCTCTTGATTA[T/C]
GTGGAATGCACTGTTCTCAAGCAGTAGGTGCCACAAGCGATGGGCTTCTCAGCTCATCATGTTCACCACTCAGGGCCGAATGAAAAGCCCACCGACGCAG

Reverse complement sequence

CTGCGTCGGTGGGCTTTTCATTCGGCCCTGAGTGGTGAACATGATGAGCTGAGAAGCCCATCGCTTGTGGCACCTACTGCTTGAGAACAGTGCATTCCAC[A/G]
TAATCAAGAGAGAGACTAGAGGATAGGATACTTAAGGGTGTGTTTGGTTCACGGTCATGCATGGATGGGATATGTCCATACATATTTTGATGGATATGGC

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	52.40%	47.10%	0.23%	0.30%	NA
All Indica	2759	84.00%	15.40%	0.18%	0.40%	NA
All Japonica	1512	5.10%	94.60%	0.26%	0.00%	NA
Aus	269	16.00%	83.60%	0.00%	0.37%	NA
Indica I	595	97.50%	2.20%	0.17%	0.17%	NA
Indica II	465	87.70%	12.30%	0.00%	0.00%	NA
Indica III	913	76.70%	22.30%	0.22%	0.77%	NA
Indica Intermediate	786	80.00%	19.30%	0.25%	0.38%	NA
Temperate Japonica	767	2.20%	97.80%	0.00%	0.00%	NA
Tropical Japonica	504	10.50%	89.50%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	95.40%	1.66%	0.00%	NA
VI/Aromatic	96	8.30%	90.60%	1.04%	0.00%	NA
Intermediate	90	35.60%	61.10%	1.11%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0814414168	T -> C	LOC_Os08g23810.1	upstream_gene_variant ; 168.0bp to feature; MODIFIER	silent_mutation	Average:95.403; most accessible tissue: Minghui63 root, score: 98.079	N	N	N	N
vg0814414168	T -> C	LOC_Os08g23810.2	upstream_gene_variant ; 168.0bp to feature; MODIFIER	silent_mutation	Average:95.403; most accessible tissue: Minghui63 root, score: 98.079	N	N	N	N
vg0814414168	T -> C	LOC_Os08g23800.1	downstream_gene_variant ; 3583.0bp to feature; MODIFIER	silent_mutation	Average:95.403; most accessible tissue: Minghui63 root, score: 98.079	N	N	N	N
vg0814414168	T -> C	LOC_Os08g23800-LOC_Os08g23810	intergenic_region ; MODIFIER	silent_mutation	Average:95.403; most accessible tissue: Minghui63 root, score: 98.079	N	N	N	N
vg0814414168	T -> DEL	N	N	silent_mutation	Average:95.403; most accessible tissue: Minghui63 root, score: 98.079	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)
vg0814414168	T	C	0.08	0.08	0.06	0.03	0.04	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0814414168	NA	8.04E-07	mr1238	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
vg0814414168	NA	6.74E-06	mr1309	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
vg0814414168	NA	7.15E-17	mr1484	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
vg0814414168	NA	6.89E-06	mr1484	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
vg0814414168	NA	1.82E-12	mr1609	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
vg0814414168	NA	3.47E-25	mr1841	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
vg0814414168	NA	2.58E-07	mr1841	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
vg0814414168	NA	1.61E-11	mr1883	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
vg0814414168	5.95E-06	5.95E-06	mr1900	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
vg0814414168	NA	2.16E-10	mr1945	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
vg0814414168	NA	2.14E-06	mr1841_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