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Detailed information for vg0518861673:

Variant ID: vg0518861673 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 18861673
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

AAATTTGTGCAAATATAAAAATTTAAAAGTTATGCTTAAAGTATTTTGGGTAATAAAGTAAGTCACAGATAAAATAAATAATAATTTCAATTTTTTTTGA[G/A]
TAAGACGAATGATCAAATAGTGCAAATAAAATATCAAAATCCCTCGTATTAGGGGATGAAGGGAGTACACTGTACTAGTACTTCCTCCGTTCCATAAAAA

Reverse complement sequence

TTTTTATGGAACGGAGGAAGTACTAGTACAGTGTACTCCCTTCATCCCCTAATACGAGGGATTTTGATATTTTATTTGCACTATTTGATCATTCGTCTTA[C/T]
TCAAAAAAAATTGAAATTATTATTTATTTTATCTGTGACTTACTTTATTACCCAAAATACTTTAAGCATAACTTTTAAATTTTTATATTTGCACAAATTT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.70%	34.20%	0.08%	0.00%	NA
All Indica	2759	98.70%	1.20%	0.11%	0.00%	NA
All Japonica	1512	3.90%	96.10%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	1.30%	0.38%	0.00%	NA
Temperate Japonica	767	3.70%	96.30%	0.00%	0.00%	NA
Tropical Japonica	504	5.40%	94.60%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	5.20%	94.80%	0.00%	0.00%	NA
Intermediate	90	57.80%	41.10%	1.11%	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
vg0518861673	G -> A	LOC_Os05g32350.1	upstream_gene_variant ; 964.0bp to feature; MODIFIER	silent_mutation	Average:86.61; most accessible tissue: Minghui63 panicle, score: 93.936	N	N	N	N
vg0518861673	G -> A	LOC_Os05g32340.1	downstream_gene_variant ; 2251.0bp to feature; MODIFIER	silent_mutation	Average:86.61; most accessible tissue: Minghui63 panicle, score: 93.936	N	N	N	N
vg0518861673	G -> A	LOC_Os05g32340-LOC_Os05g32350	intergenic_region ; MODIFIER	silent_mutation	Average:86.61; most accessible tissue: Minghui63 panicle, score: 93.936	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)
vg0518861673	G	A	-0.03	-0.01	-0.01	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0518861673	NA	1.75E-76	mr1135	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
vg0518861673	NA	3.16E-07	mr1162	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
vg0518861673	NA	9.58E-87	mr1504	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
vg0518861673	NA	2.54E-91	mr1517	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
vg0518861673	NA	5.80E-72	mr1538	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
vg0518861673	NA	2.87E-22	mr1541	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
vg0518861673	NA	1.01E-19	mr1588	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
vg0518861673	NA	2.70E-57	mr1594	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
vg0518861673	NA	2.84E-10	mr1630	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
vg0518861673	NA	5.07E-12	mr1636	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
vg0518861673	NA	5.47E-86	mr1672	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
vg0518861673	NA	1.70E-30	mr1737	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
vg0518861673	NA	3.22E-91	mr1758	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
vg0518861673	NA	1.14E-104	mr1538_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
vg0518861673	NA	6.21E-38	mr1541_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