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Detailed information for vg0404517226:

Variant ID: vg0404517226 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 4517226
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.53, C: 0.47, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTCCACCTCCTGCATAGTCGCTGCTACCCTGCCGGGTTAATGGCCCTGGCGAGGCCTCCCCCAAGGTTGTGGTGCTGAGTGCCCCTGCCCCACCATCT[T/C]
CCTCGTCTCCAGCGGCTCCCCACCGTCGGATATCACTGGCCGCCGCCTCCTAACCAGTCTCGTTGTTTTCTCCCGCCGCCAAAGCCGGCCCTCCACCTGC

Reverse complement sequence

GCAGGTGGAGGGCCGGCTTTGGCGGCGGGAGAAAACAACGAGACTGGTTAGGAGGCGGCGGCCAGTGATATCCGACGGTGGGGAGCCGCTGGAGACGAGG[A/G]
AGATGGTGGGGCAGGGGCACTCAGCACCACAACCTTGGGGGAGGCCTCGCCAGGGCCATTAACCCGGCAGGGTAGCAGCGACTATGCAGGAGGTGGAGCA

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	56.40%	43.50%	0.08%	0.00%	NA
All Indica	2759	37.00%	62.80%	0.11%	0.00%	NA
All Japonica	1512	89.30%	10.60%	0.07%	0.00%	NA
Aus	269	53.90%	46.10%	0.00%	0.00%	NA
Indica I	595	5.40%	94.60%	0.00%	0.00%	NA
Indica II	465	72.90%	27.10%	0.00%	0.00%	NA
Indica III	913	34.60%	65.30%	0.11%	0.00%	NA
Indica Intermediate	786	42.60%	57.10%	0.25%	0.00%	NA
Temperate Japonica	767	98.40%	1.40%	0.13%	0.00%	NA
Tropical Japonica	504	82.50%	17.50%	0.00%	0.00%	NA
Japonica Intermediate	241	74.30%	25.70%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	73.30%	26.70%	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
vg0404517226	T -> C	LOC_Os04g08410.1	upstream_gene_variant ; 3343.0bp to feature; MODIFIER	silent_mutation	Average:76.512; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N
vg0404517226	T -> C	LOC_Os04g08415.1	downstream_gene_variant ; 3533.0bp to feature; MODIFIER	silent_mutation	Average:76.512; most accessible tissue: Zhenshan97 young leaf, score: 88.127	N	N	N	N
vg0404517226	T -> C	LOC_Os04g08410-LOC_Os04g08415	intergenic_region ; MODIFIER	silent_mutation	Average:76.512; most accessible tissue: Zhenshan97 young leaf, score: 88.127	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)
vg0404517226	T	C	0.01	0.0	0.0	0.01	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0404517226	NA	5.43E-15	mr1535	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
vg0404517226	NA	3.22E-06	mr1608	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
vg0404517226	NA	5.21E-07	mr1835	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
vg0404517226	NA	7.49E-06	mr1835	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
vg0404517226	NA	2.89E-10	mr1904	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
vg0404517226	NA	3.84E-06	mr1072_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
vg0404517226	NA	4.15E-06	mr1075_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
vg0404517226	NA	2.33E-06	mr1149_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
vg0404517226	NA	3.64E-06	mr1441_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
vg0404517226	2.58E-06	4.32E-08	mr1595_2	Jap_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
vg0404517226	NA	5.74E-10	mr1835_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
vg0404517226	NA	2.36E-06	mr1835_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
vg0404517226	NA	5.64E-13	mr1904_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