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Detailed information for vg0434837711:

Variant ID: vg0434837711 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 34837711
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.40, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

AATTTGATGGATTAGATTAAATCCAATCCCTTTTTCCCTGGTTACTACTAGCCCATTTTCTTTCAAAAGAAATACTACAATGTAGAGTCTATAAAAAAAT[A/G]
TTATCTAGTACAGTAGAGAACATGTTACCTTTAAACTTTCTGACAACAATTAGATAAGAACAAACAAAACAAAAACATTGCACCGATAGAAGCTTCTTGT

Reverse complement sequence

ACAAGAAGCTTCTATCGGTGCAATGTTTTTGTTTTGTTTGTTCTTATCTAATTGTTGTCAGAAAGTTTAAAGGTAACATGTTCTCTACTGTACTAGATAA[T/C]
ATTTTTTTATAGACTCTACATTGTAGTATTTCTTTTGAAAGAAAATGGGCTAGTAGTAACCAGGGAAAAAGGGATTGGATTTAATCTAATCCATCAAATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.10%	36.60%	0.30%	0.00%	NA
All Indica	2759	94.50%	5.00%	0.43%	0.00%	NA
All Japonica	1512	1.40%	98.60%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	97.10%	2.40%	0.50%	0.00%	NA
Indica II	465	98.10%	1.50%	0.43%	0.00%	NA
Indica III	913	94.30%	5.70%	0.00%	0.00%	NA
Indica Intermediate	786	90.70%	8.40%	0.89%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	2.60%	97.40%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	43.80%	55.20%	1.04%	0.00%	NA
Intermediate	90	48.90%	50.00%	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
vg0434837711	A -> G	LOC_Os04g58590.1	upstream_gene_variant ; 368.0bp to feature; MODIFIER	silent_mutation	Average:64.229; most accessible tissue: Minghui63 panicle, score: 93.63	N	N	N	N
vg0434837711	A -> G	LOC_Os04g58600.2	upstream_gene_variant ; 1785.0bp to feature; MODIFIER	silent_mutation	Average:64.229; most accessible tissue: Minghui63 panicle, score: 93.63	N	N	N	N
vg0434837711	A -> G	LOC_Os04g58590-LOC_Os04g58600	intergenic_region ; MODIFIER	silent_mutation	Average:64.229; most accessible tissue: Minghui63 panicle, score: 93.63	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)
vg0434837711	A	G	0.0	-0.01	-0.01	0.01	0.02	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0434837711	NA	5.57E-09	mr1302	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
vg0434837711	NA	2.45E-07	mr1604	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
vg0434837711	NA	3.26E-19	mr1627	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
vg0434837711	NA	9.98E-07	mr1646	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
vg0434837711	NA	6.37E-11	mr1683	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
vg0434837711	NA	1.05E-23	mr1917	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
vg0434837711	NA	3.18E-13	mr1924	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
vg0434837711	6.36E-06	NA	mr1068_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
vg0434837711	6.80E-08	NA	mr1090_2	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
vg0434837711	NA	5.93E-14	mr1575_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
vg0434837711	NA	1.94E-21	mr1627_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
vg0434837711	NA	1.00E-09	mr1646_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
vg0434837711	NA	1.22E-23	mr1708_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