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Detailed information for vg0204236567:

Variant ID: vg0204236567 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 4236567
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CACCTCCCCATTCGCCTCCCTCATCAGTGCCCTTCTCGCCGCCCACCGCATCTAGCTCAACGAGATGGGGAAGAGAGGAGAGGGGACGATGAAGGAAGAA[A/G]
ATTGAACTGACATGTCGGTCCCACATCTAGAGATATTTTGGTCTATATGATGACAGAAAATATGATGTGATGGTATGTTCTAATTTTGTACATATTTAGG

Reverse complement sequence

CCTAAATATGTACAAAATTAGAACATACCATCACATCATATTTTCTGTCATCATATAGACCAAAATATCTCTAGATGTGGGACCGACATGTCAGTTCAAT[T/C]
TTCTTCCTTCATCGTCCCCTCTCCTCTCTTCCCCATCTCGTTGAGCTAGATGCGGTGGGCGGCGAGAAGGGCACTGATGAGGGAGGCGAATGGGGAGGTG

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	88.60%	9.20%	2.26%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	65.50%	27.70%	6.81%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	47.30%	42.80%	9.91%	0.00%	NA
Tropical Japonica	504	94.40%	3.20%	2.38%	0.00%	NA
Japonica Intermediate	241	62.70%	31.10%	6.22%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	85.60%	11.10%	3.33%	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
vg0204236567	A -> G	LOC_Os02g08040.1	downstream_gene_variant ; 1483.0bp to feature; MODIFIER	silent_mutation	Average:77.362; most accessible tissue: Callus, score: 95.749	N	N	N	N
vg0204236567	A -> G	LOC_Os02g08050.1	downstream_gene_variant ; 2486.0bp to feature; MODIFIER	silent_mutation	Average:77.362; most accessible tissue: Callus, score: 95.749	N	N	N	N
vg0204236567	A -> G	LOC_Os02g08040-LOC_Os02g08050	intergenic_region ; MODIFIER	silent_mutation	Average:77.362; most accessible tissue: Callus, score: 95.749	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)
vg0204236567	A	G	-0.03	-0.06	-0.04	-0.04	-0.05	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0204236567	NA	1.66E-07	mr1002	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
vg0204236567	NA	9.38E-08	mr1045	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
vg0204236567	NA	2.29E-06	mr1045	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
vg0204236567	NA	5.51E-06	mr1070	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
vg0204236567	NA	2.75E-06	mr1097	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
vg0204236567	9.68E-06	9.68E-06	mr1128	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
vg0204236567	NA	1.81E-06	mr1252	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
vg0204236567	NA	6.97E-06	mr1708	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
vg0204236567	1.36E-08	NA	mr1745	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
vg0204236567	NA	4.81E-07	mr1748	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
vg0204236567	4.47E-07	1.47E-08	mr1872	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
vg0204236567	NA	2.83E-06	mr1903	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
vg0204236567	NA	1.10E-06	mr1910	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