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Detailed information for vg0138058961:

Variant ID: vg0138058961 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 38058961
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGTAATGGCTACTGCAGTGTCACCATGTGAAATACATCCAAACTTATCTTTCATTTGCAGCACTCAACTTTTTTTATGCTTGTTGTGTGATATTTTTT[T/A]
AAAAAAATATATACCGCGAATTTAAACCATGAAATCAAAATGTCAATAAGTATATGGGGGTTGGTACCTAAAATATTTTTTCCCTGTATTTGAAAGGTAT

Reverse complement sequence

ATACCTTTCAAATACAGGGAAAAAATATTTTAGGTACCAACCCCCATATACTTATTGACATTTTGATTTCATGGTTTAAATTCGCGGTATATATTTTTTT[A/T]
AAAAAATATCACACAACAAGCATAAAAAAAGTTGAGTGCTGCAAATGAAAGATAAGTTTGGATGTATTTCACATGGTGACACTGCAGTAGCCATTACATG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	65.90%	32.40%	1.63%	0.00%	NA
All Indica	2759	97.00%	2.80%	0.25%	0.00%	NA
All Japonica	1512	9.10%	86.40%	4.50%	0.00%	NA
Aus	269	95.20%	4.50%	0.37%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	98.70%	0.90%	0.43%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	92.00%	7.40%	0.64%	0.00%	NA
Temperate Japonica	767	14.00%	77.40%	8.60%	0.00%	NA
Tropical Japonica	504	3.60%	96.20%	0.20%	0.00%	NA
Japonica Intermediate	241	5.40%	94.20%	0.41%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	50.00%	48.90%	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
vg0138058961	T -> A	LOC_Os01g65560.1	upstream_gene_variant ; 1119.0bp to feature; MODIFIER	silent_mutation	Average:77.882; most accessible tissue: Minghui63 flower, score: 88.913	N	N	N	N
vg0138058961	T -> A	LOC_Os01g65550.1	downstream_gene_variant ; 4604.0bp to feature; MODIFIER	silent_mutation	Average:77.882; most accessible tissue: Minghui63 flower, score: 88.913	N	N	N	N
vg0138058961	T -> A	LOC_Os01g65550.2	downstream_gene_variant ; 4604.0bp to feature; MODIFIER	silent_mutation	Average:77.882; most accessible tissue: Minghui63 flower, score: 88.913	N	N	N	N
vg0138058961	T -> A	LOC_Os01g65560-LOC_Os01g65580	intergenic_region ; MODIFIER	silent_mutation	Average:77.882; most accessible tissue: Minghui63 flower, score: 88.913	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)
vg0138058961	T	A	0.0	0.0	0.0	0.0	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0138058961	1.35E-06	NA	Awn_length	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
vg0138058961	NA	1.14E-08	Awn_length	Jap_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
vg0138058961	2.17E-06	NA	mr1446	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