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Detailed information for vg0604320247:

Variant ID: vg0604320247 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4320247
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGAAGCGGATAAGGCGTGGGACTAAAACTTTTCAAGTCCCTATCACATCAGATGTTTGGACTCTAATTATAAATATTAAACGTAGACTATTAATAAAAC[T/C]
CATCCATAATCTTGGACTAATTCGCGAGACGAATCTATTGAGCCTAATTAATCCATAATTAGCCTATGTGATGCTACAGTAAATATTCACTAATTATTGA

Reverse complement sequence

TCAATAATTAGTGAATATTTACTGTAGCATCACATAGGCTAATTATGGATTAATTAGGCTCAATAGATTCGTCTCGCGAATTAGTCCAAGATTATGGATG[A/G]
GTTTTATTAATAGTCTACGTTTAATATTTATAATTAGAGTCCAAACATCTGATGTGATAGGGACTTGAAAAGTTTTAGTCCCACGCCTTATCCGCTTCGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	12.30%	7.60%	2.16%	77.87%	NA
All Indica	2759	0.70%	5.10%	0.25%	93.95%	NA
All Japonica	1512	37.00%	13.20%	6.15%	43.58%	NA
Aus	269	0.00%	0.40%	0.00%	99.63%	NA
Indica I	595	0.30%	0.00%	0.34%	99.33%	NA
Indica II	465	0.40%	11.00%	0.43%	88.17%	NA
Indica III	913	0.40%	3.20%	0.00%	96.39%	NA
Indica Intermediate	786	1.50%	7.60%	0.38%	90.46%	NA
Temperate Japonica	767	63.20%	18.60%	9.91%	8.21%	NA
Tropical Japonica	504	3.20%	4.60%	0.60%	91.67%	NA
Japonica Intermediate	241	24.50%	14.10%	5.81%	55.60%	NA
VI/Aromatic	96	0.00%	12.50%	0.00%	87.50%	NA
Intermediate	90	3.30%	8.90%	2.22%	85.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0604320247	T -> C	LOC_Os06g08660.1	upstream_gene_variant ; 998.0bp to feature; MODIFIER	silent_mutation	Average:88.476; most accessible tissue: Zhenshan97 flag leaf, score: 96.346	N	N	N	N
vg0604320247	T -> C	LOC_Os06g08670.1	upstream_gene_variant ; 1360.0bp to feature; MODIFIER	silent_mutation	Average:88.476; most accessible tissue: Zhenshan97 flag leaf, score: 96.346	N	N	N	N
vg0604320247	T -> C	LOC_Os06g08650.1	downstream_gene_variant ; 3651.0bp to feature; MODIFIER	silent_mutation	Average:88.476; most accessible tissue: Zhenshan97 flag leaf, score: 96.346	N	N	N	N
vg0604320247	T -> C	LOC_Os06g08660-LOC_Os06g08670	intergenic_region ; MODIFIER	silent_mutation	Average:88.476; most accessible tissue: Zhenshan97 flag leaf, score: 96.346	N	N	N	N
vg0604320247	T -> DEL	N	N	silent_mutation	Average:88.476; most accessible tissue: Zhenshan97 flag leaf, score: 96.346	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)
vg0604320247	T	C	0.05	0.06	0.05	0.02	0.04	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604320247	NA	2.91E-09	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
vg0604320247	2.47E-08	NA	mr1137	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
vg0604320247	4.76E-07	NA	mr1137	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
vg0604320247	NA	2.34E-06	mr1201	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
vg0604320247	3.66E-06	1.27E-06	mr1274	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
vg0604320247	6.88E-08	NA	mr1617	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
vg0604320247	5.88E-07	1.64E-07	mr1617	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
vg0604320247	NA	8.10E-06	mr1750	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
vg0604320247	1.81E-09	NA	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
vg0604320247	4.23E-06	6.76E-08	mr1137_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