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Detailed information for vg1227491928:

Variant ID: vg1227491928 (JBrowse)	Variation Type: INDEL
Chromosome: chr12	Position: 27491928
Reference Allele: A	Alternative Allele: AGAGGGAG
Primary Allele: A	Secondary Allele: AGAGGGAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCACAGAAACTGTCATCCTTGGCCATTGCTAGCTGCTAGCTGTTACAAGGTTTGTTGGGTAGCCTAGCTACACAAGAAAGAGAAGGAGGAGGAGAAGGA[A/AGAGGGAG]
GAGGGAGGAGGAAAAGAAAGAAGAGCTAGAGAAGAAGTTTGTTGTATTTGCAGTAGTAAGAAGAAAGAAAGAAAGTAGCAGGTAGAGAGAGAGATGGCGG

Reverse complement sequence

CCGCCATCTCTCTCTCTACCTGCTACTTTCTTTCTTTCTTCTTACTACTGCAAATACAACAAACTTCTTCTCTAGCTCTTCTTTCTTTTCCTCCTCCCTC[T/CTCCCTCT]
TCCTTCTCCTCCTCCTTCTCTTTCTTGTGTAGCTAGGCTACCCAACAAACCTTGTAACAGCTAGCAGCTAGCAATGGCCAAGGATGACAGTTTCTGTGCC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of AGAGGGAG(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	37.20%	2.50%	2.03%	58.25%	NA
All Indica	2759	4.50%	0.60%	1.20%	93.73%	NA
All Japonica	1512	99.20%	0.00%	0.00%	0.79%	NA
Aus	269	4.10%	35.70%	21.19%	39.03%	NA
Indica I	595	2.20%	0.20%	1.01%	96.64%	NA
Indica II	465	4.50%	0.00%	1.94%	93.55%	NA
Indica III	913	4.70%	0.50%	1.31%	93.43%	NA
Indica Intermediate	786	6.00%	1.30%	0.76%	91.98%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	99.20%	0.00%	0.00%	0.79%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	81.20%	5.20%	5.21%	8.33%	NA
Intermediate	90	52.20%	0.00%	1.11%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1227491928	A -> DEL	N	N	silent_mutation	Average:91.136; most accessible tissue: Zhenshan97 flower, score: 95.036	N	N	N	N
vg1227491928	A -> AGAGGGAG	LOC_Os12g44350.1	5_prime_UTR_variant ; 82.0bp to feature; MODIFIER	silent_mutation	Average:91.136; most accessible tissue: Zhenshan97 flower, score: 95.036	N	N	N	N
vg1227491928	A -> AGAGGGAG	LOC_Os12g44340.1	downstream_gene_variant ; 339.0bp to feature; MODIFIER	silent_mutation	Average:91.136; most accessible tissue: Zhenshan97 flower, score: 95.036	N	N	N	N
vg1227491928	A -> AGAGGGAG	LOC_Os12g44360.1	downstream_gene_variant ; 3832.0bp to feature; MODIFIER	silent_mutation	Average:91.136; most accessible tissue: Zhenshan97 flower, score: 95.036	N	N	N	N
vg1227491928	A -> AGAGGGAG	LOC_Os12g44360.2	downstream_gene_variant ; 2472.0bp to feature; MODIFIER	silent_mutation	Average:91.136; most accessible tissue: Zhenshan97 flower, score: 95.036	N	N	N	N
vg1227491928	A -> AGAGGGAG	LOC_Os12g44360.3	downstream_gene_variant ; 3832.0bp to feature; MODIFIER	silent_mutation	Average:91.136; most accessible tissue: Zhenshan97 flower, score: 95.036	N	N	N	N
vg1227491928	A -> AGAGGGAG	LOC_Os12g44360.4	downstream_gene_variant ; 3832.0bp to feature; MODIFIER	silent_mutation	Average:91.136; most accessible tissue: Zhenshan97 flower, score: 95.036	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)
vg1227491928	A	AGAGG*	0.1	-0.04	-0.08	-0.04	-0.06	-0.15

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1227491928	6.92E-06	NA	mr1151_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
vg1227491928	2.37E-06	6.90E-07	mr1263_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