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Detailed information for vg0221956507:

Variant ID: vg0221956507 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21956507
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCCAACGTCTAAAACTGGGTACCAAGGTCAGAATGTATGGTATTCGTGAGAAAGGTAGTACTCCCTCCAGCCTGTTATAAGCGCAACCATAGCCCGTAAG[T/G]
TGTTCAACTTTAAACGTTCATCTTATTTAAATTTTTTTTATGATTTGTATTTTTATTGTTATTAGATGATAAAACATGAATAACCCAAGGGAAATCAGCA

Reverse complement sequence

TGCTGATTTCCCTTGGGTTATTCATGTTTTATCATCTAATAACAATAAAAATACAAATCATAAAAAAAATTTAAATAAGATGAACGTTTAAAGTTGAACA[A/C]
CTTACGGGCTATGGTTGCGCTTATAACAGGCTGGAGGGAGTACTACCTTTCTCACGAATACCATACATTCTGACCTTGGTACCCAGTTTTAGACGTTGGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.80%	33.30%	0.99%	20.84%	NA
All Indica	2759	54.80%	9.20%	1.41%	34.58%	NA
All Japonica	1512	19.20%	79.60%	0.20%	0.93%	NA
Aus	269	99.30%	0.40%	0.00%	0.37%	NA
Indica I	595	80.80%	1.80%	0.34%	16.97%	NA
Indica II	465	43.40%	1.50%	2.58%	52.47%	NA
Indica III	913	42.10%	16.90%	0.99%	40.09%	NA
Indica Intermediate	786	56.60%	10.40%	2.04%	30.92%	NA
Temperate Japonica	767	23.10%	76.50%	0.13%	0.26%	NA
Tropical Japonica	504	18.30%	79.80%	0.00%	1.98%	NA
Japonica Intermediate	241	9.10%	89.20%	0.83%	0.83%	NA
VI/Aromatic	96	8.30%	90.60%	1.04%	0.00%	NA
Intermediate	90	45.60%	32.20%	4.44%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0221956507	T -> G	LOC_Os02g36350.1	upstream_gene_variant ; 4732.0bp to feature; MODIFIER	silent_mutation	Average:83.662; most accessible tissue: Callus, score: 95.003	N	N	N	N
vg0221956507	T -> G	LOC_Os02g36350.2	upstream_gene_variant ; 4732.0bp to feature; MODIFIER	silent_mutation	Average:83.662; most accessible tissue: Callus, score: 95.003	N	N	N	N
vg0221956507	T -> G	LOC_Os02g36360.1	downstream_gene_variant ; 81.0bp to feature; MODIFIER	silent_mutation	Average:83.662; most accessible tissue: Callus, score: 95.003	N	N	N	N
vg0221956507	T -> G	LOC_Os02g36360.2	downstream_gene_variant ; 82.0bp to feature; MODIFIER	silent_mutation	Average:83.662; most accessible tissue: Callus, score: 95.003	N	N	N	N
vg0221956507	T -> G	LOC_Os02g36360.3	downstream_gene_variant ; 82.0bp to feature; MODIFIER	silent_mutation	Average:83.662; most accessible tissue: Callus, score: 95.003	N	N	N	N
vg0221956507	T -> G	LOC_Os02g36350-LOC_Os02g36360	intergenic_region ; MODIFIER	silent_mutation	Average:83.662; most accessible tissue: Callus, score: 95.003	N	N	N	N
vg0221956507	T -> DEL	N	N	silent_mutation	Average:83.662; most accessible tissue: Callus, score: 95.003	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)
vg0221956507	T	G	0.02	0.05	0.03	0.04	0.04	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221956507	5.92E-08	7.89E-10	Awn_length	Ind_All	YES	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
vg0221956507	NA	5.41E-06	mr1072	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
vg0221956507	NA	1.25E-06	mr1124	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
vg0221956507	NA	3.57E-15	mr1592	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
vg0221956507	NA	4.82E-11	mr1595_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
vg0221956507	NA	6.07E-10	mr1600_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
vg0221956507	NA	1.64E-06	mr1936_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