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Detailed information for vg0610487848:

Variant ID: vg0610487848 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10487848
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTACAGTCATTTGAGTCTGTCACTACAGTGGTTTGCATTATCACAGTAGCACGGTTACTATAGCAACAGTGTTCTAGTTACTCTAGGTACTGATTTGTAC[C/T]
GTTGGATGAAGATCCATCGCATAAAACATGAGCCAATGCAAGATACAGTACCACCTCTGCATTTTCTTTTTCAATGCAGAAAATCTCAATCCCTAGAGCG

Reverse complement sequence

CGCTCTAGGGATTGAGATTTTCTGCATTGAAAAAGAAAATGCAGAGGTGGTACTGTATCTTGCATTGGCTCATGTTTTATGCGATGGATCTTCATCCAAC[G/A]
GTACAAATCAGTACCTAGAGTAACTAGAACACTGTTGCTATAGTAACCGTGCTACTGTGATAATGCAAACCACTGTAGTGACAGACTCAAATGACTGTAC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.90%	0.70%	2.94%	36.39%	NA
All Indica	2759	74.20%	0.30%	1.34%	24.25%	NA
All Japonica	1512	42.90%	0.90%	3.77%	52.45%	NA
Aus	269	24.90%	4.50%	10.78%	59.85%	NA
Indica I	595	94.50%	0.30%	0.50%	4.71%	NA
Indica II	465	90.80%	0.20%	0.43%	8.60%	NA
Indica III	913	57.40%	0.30%	1.64%	40.64%	NA
Indica Intermediate	786	68.40%	0.10%	2.16%	29.26%	NA
Temperate Japonica	767	58.00%	0.50%	3.26%	38.20%	NA
Tropical Japonica	504	28.00%	1.00%	3.97%	67.06%	NA
Japonica Intermediate	241	25.70%	2.10%	4.98%	67.22%	NA
VI/Aromatic	96	9.40%	1.00%	13.54%	76.04%	NA
Intermediate	90	68.90%	1.10%	3.33%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610487848	C -> T	LOC_Os06g18020.1	upstream_gene_variant ; 600.0bp to feature; MODIFIER	silent_mutation	Average:85.331; most accessible tissue: Minghui63 panicle, score: 98.323	N	N	N	N
vg0610487848	C -> T	LOC_Os06g18010-LOC_Os06g18020	intergenic_region ; MODIFIER	silent_mutation	Average:85.331; most accessible tissue: Minghui63 panicle, score: 98.323	N	N	N	N
vg0610487848	C -> DEL	N	N	silent_mutation	Average:85.331; most accessible tissue: Minghui63 panicle, score: 98.323	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)
vg0610487848	C	T	-0.02	-0.03	-0.02	0.03	0.02	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610487848	3.46E-06	NA	mr1261	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