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Detailed information for vg0809743223:

Variant ID: vg0809743223 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9743223
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGATCATGAATTAATCCAAATACTCGGATAATATTTCTTCAAGTATTTACCATTAAGCGTTCGTCCATAAACTTCACCATCAAGCCCTTGCAACATATAT[G/A]
CTCCCTTAGAAACAACCTTATGAATCTGGAACGGTCCTTCTGTAACGCCCCGACATTCATTAGCCATTAACACAGCTAAATCACACCGGGGTGTTATGCA

Reverse complement sequence

TGCATAACACCCCGGTGTGATTTAGCTGTGTTAATGGCTAATGAATGTCGGGGCGTTACAGAAGGACCGTTCCAGATTCATAAGGTTGTTTCTAAGGGAG[C/T]
ATATATGTTGCAAGGGCTTGATGGTGAAGTTTATGGACGAACGCTTAATGGTAAATACTTGAAGAAATATTATCCGAGTATTTGGATTAATTCATGATCG

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	84.00%	8.80%	6.24%	0.95%	NA
All Indica	2759	96.30%	0.10%	3.52%	0.00%	NA
All Japonica	1512	65.10%	26.40%	5.69%	2.84%	NA
Aus	269	59.50%	0.00%	39.78%	0.74%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	88.40%	0.40%	11.18%	0.00%	NA
Indica III	913	99.00%	0.10%	0.88%	0.00%	NA
Indica Intermediate	786	95.20%	0.10%	4.71%	0.00%	NA
Temperate Japonica	767	95.20%	2.30%	1.43%	1.04%	NA
Tropical Japonica	504	29.60%	52.00%	11.90%	6.55%	NA
Japonica Intermediate	241	43.60%	49.40%	6.22%	0.83%	NA
VI/Aromatic	96	94.80%	3.10%	2.08%	0.00%	NA
Intermediate	90	84.40%	12.20%	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
vg0809743223	G -> A	LOC_Os08g15990.1	downstream_gene_variant ; 507.0bp to feature; MODIFIER	silent_mutation	Average:62.429; most accessible tissue: Zhenshan97 flag leaf, score: 91.894	N	N	N	N
vg0809743223	G -> A	LOC_Os08g16000.1	downstream_gene_variant ; 3726.0bp to feature; MODIFIER	silent_mutation	Average:62.429; most accessible tissue: Zhenshan97 flag leaf, score: 91.894	N	N	N	N
vg0809743223	G -> A	LOC_Os08g15990-LOC_Os08g16000	intergenic_region ; MODIFIER	silent_mutation	Average:62.429; most accessible tissue: Zhenshan97 flag leaf, score: 91.894	N	N	N	N
vg0809743223	G -> DEL	N	N	silent_mutation	Average:62.429; most accessible tissue: Zhenshan97 flag leaf, score: 91.894	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)
vg0809743223	G	A	0.0	0.0	0.0	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809743223	NA	1.18E-11	Grain_weight	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0809743223	NA	8.26E-06	mr1095	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
vg0809743223	NA	4.02E-06	mr1887	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
vg0809743223	NA	6.72E-09	mr1194_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
vg0809743223	NA	9.38E-06	mr1383_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
vg0809743223	NA	9.15E-06	mr1482_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
vg0809743223	NA	1.15E-09	mr1769_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
vg0809743223	NA	3.05E-22	mr1871_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