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Detailed information for vg0813117473:

Variant ID: vg0813117473 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 13117473
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTTAGGTTCAACTGGCTGGTGCTTGCTGGTGCATGTAACTTAATAATCCGCGTCGCGTGTATGTTGAGCAAGGCGTTGCCGCCGCAAGTGCTGGTAGC[T/C]
AGCGGCGATTGGCGATGCGTACGGTGCACAGGATGCGCCAGCCATGCGTGGCCGCGATGTAGGCGCCGCAGACGAGCTCGAGTTTGCTTGGGCAGGGCAC

Reverse complement sequence

GTGCCCTGCCCAAGCAAACTCGAGCTCGTCTGCGGCGCCTACATCGCGGCCACGCATGGCTGGCGCATCCTGTGCACCGTACGCATCGCCAATCGCCGCT[A/G]
GCTACCAGCACTTGCGGCGGCAACGCCTTGCTCAACATACACGCGACGCGGATTATTAAGTTACATGCACCAGCAAGCACCAGCCAGTTGAACCTAAAAG

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	61.50%	22.40%	0.42%	15.68%	NA
All Indica	2759	90.30%	0.70%	0.29%	8.70%	NA
All Japonica	1512	12.60%	65.90%	0.46%	21.03%	NA
Aus	269	56.10%	0.40%	1.86%	41.64%	NA
Indica I	595	97.50%	0.70%	0.00%	1.85%	NA
Indica II	465	92.00%	1.50%	0.86%	5.59%	NA
Indica III	913	84.60%	0.30%	0.22%	14.90%	NA
Indica Intermediate	786	90.60%	0.60%	0.25%	8.52%	NA
Temperate Japonica	767	5.60%	85.40%	0.13%	8.87%	NA
Tropical Japonica	504	21.00%	42.70%	0.99%	35.32%	NA
Japonica Intermediate	241	17.00%	52.70%	0.41%	29.88%	NA
VI/Aromatic	96	20.80%	17.70%	0.00%	61.46%	NA
Intermediate	90	57.80%	28.90%	0.00%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0813117473	T -> C	LOC_Os08g21890.1	upstream_gene_variant ; 3993.0bp to feature; MODIFIER	silent_mutation	Average:80.873; most accessible tissue: Zhenshan97 flag leaf, score: 90.842	N	N	N	N
vg0813117473	T -> C	LOC_Os08g21900.1	downstream_gene_variant ; 2168.0bp to feature; MODIFIER	silent_mutation	Average:80.873; most accessible tissue: Zhenshan97 flag leaf, score: 90.842	N	N	N	N
vg0813117473	T -> C	LOC_Os08g21890-LOC_Os08g21900	intergenic_region ; MODIFIER	silent_mutation	Average:80.873; most accessible tissue: Zhenshan97 flag leaf, score: 90.842	N	N	N	N
vg0813117473	T -> DEL	N	N	silent_mutation	Average:80.873; most accessible tissue: Zhenshan97 flag leaf, score: 90.842	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)
vg0813117473	T	C	-0.03	-0.01	-0.01	-0.02	-0.02	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0813117473	NA	6.61E-07	mr1045_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
vg0813117473	NA	2.03E-35	mr1137_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
vg0813117473	NA	2.63E-07	mr1252_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
vg0813117473	NA	2.98E-06	mr1252_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
vg0813117473	NA	2.62E-07	mr1482_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
vg0813117473	NA	1.48E-06	mr1555_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
vg0813117473	NA	8.89E-29	mr1617_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
vg0813117473	NA	3.05E-06	mr1693_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
vg0813117473	NA	4.09E-06	mr1785_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
vg0813117473	NA	1.88E-09	mr1825_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
vg0813117473	NA	7.19E-11	mr1844_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
vg0813117473	1.54E-06	1.54E-06	mr1919_2	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
vg0813117473	NA	2.81E-06	mr1919_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