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Detailed information for vg1205680656:

Variant ID: vg1205680656 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 5680656
Reference Allele: T	Alternative Allele: C,TCA
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

AGCATATACTACTTCTGATTCTAGGTTGTTCAACAAAGATTAAAAATTGAGATAAAATTAACTTGAGATGCCCCCTGAAAGTTTACTTGAGTAGGAAAGA[T/C,TCA]
CACGTCTAGCAATGTATTCGCTCCGTCCTAAAATAGATATTAGCTATTTCTTATCTATATATGTAGCCAGAAACAACTACATTTCAGAATGGAGAGAGTA

Reverse complement sequence

TACTCTCTCCATTCTGAAATGTAGTTGTTTCTGGCTACATATATAGATAAGAAATAGCTAATATCTATTTTAGGACGGAGCGAATACATTGCTAGACGTG[A/G,TGA]
TCTTTCCTACTCAAGTAAACTTTCAGGGGGCATCTCAAGTTAATTTTATCTCAATTTTTAATCTTTGTTGAACAACCTAGAATCAGAAGTAGTATATGCT

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	60.90%	38.80%	0.08%	0.00%	TCA: 0.19%
All Indica	2759	34.30%	65.20%	0.14%	0.00%	TCA: 0.33%
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	73.40%	26.40%	0.17%	0.00%	NA
Indica II	465	22.20%	77.60%	0.22%	0.00%	NA
Indica III	913	9.20%	89.90%	0.11%	0.00%	TCA: 0.77%
Indica Intermediate	786	41.00%	58.70%	0.13%	0.00%	TCA: 0.25%
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	98.00%	2.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	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
vg1205680656	T -> C	LOC_Os12g10630.1	downstream_gene_variant ; 3180.0bp to feature; MODIFIER	silent_mutation	Average:72.146; most accessible tissue: Zhenshan97 panicle, score: 96.599	N	N	N	N
vg1205680656	T -> C	LOC_Os12g10640.1	downstream_gene_variant ; 3944.0bp to feature; MODIFIER	silent_mutation	Average:72.146; most accessible tissue: Zhenshan97 panicle, score: 96.599	N	N	N	N
vg1205680656	T -> C	LOC_Os12g10630-LOC_Os12g10640	intergenic_region ; MODIFIER	silent_mutation	Average:72.146; most accessible tissue: Zhenshan97 panicle, score: 96.599	N	N	N	N
vg1205680656	T -> TCA	LOC_Os12g10630.1	downstream_gene_variant ; 3181.0bp to feature; MODIFIER	silent_mutation	Average:72.146; most accessible tissue: Zhenshan97 panicle, score: 96.599	N	N	N	N
vg1205680656	T -> TCA	LOC_Os12g10640.1	downstream_gene_variant ; 3943.0bp to feature; MODIFIER	silent_mutation	Average:72.146; most accessible tissue: Zhenshan97 panicle, score: 96.599	N	N	N	N
vg1205680656	T -> TCA	LOC_Os12g10630-LOC_Os12g10640	intergenic_region ; MODIFIER	silent_mutation	Average:72.146; most accessible tissue: Zhenshan97 panicle, score: 96.599	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)
vg1205680656	T	C	0.03	0.02	0.01	0.04	0.05	0.03
vg1205680656	T	TCA	0.02	0.02	0.0	-0.03	0.02	0.13

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1205680656	NA	8.29E-06	mr1030	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
vg1205680656	NA	2.49E-06	mr1057	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
vg1205680656	NA	2.19E-12	mr1170	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
vg1205680656	NA	5.61E-06	mr1170	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
vg1205680656	NA	5.78E-07	mr1285	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
vg1205680656	NA	2.29E-06	mr1375	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
vg1205680656	NA	1.35E-06	mr1511	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
vg1205680656	NA	9.31E-06	mr1656	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
vg1205680656	1.75E-06	1.76E-06	mr1673	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
vg1205680656	NA	4.81E-06	mr1673	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
vg1205680656	NA	4.18E-08	mr1527_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