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Detailed information for vg0427444019:

Variant ID: vg0427444019 (JBrowse)	Variation Type: INDEL
Chromosome: chr04	Position: 27444019
Reference Allele: GTTCAAAA	Alternative Allele: ATTCAAAA,G
Primary Allele: GTTCAAAA	Secondary Allele: ATTCAAAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCTTAAATGTCGATCTTTTCTTTACTTTCTTTGTGATTATTTACGGTTTGGCAAGCAATATCAATCATAACAACCAGCATGATGCAACAGTTTTAAAAA[GTTCAAAA/ATTCAAAA,G]
TTTTAGTGATTTTTATTATTGGGAATTTTCAGGATGTTACAGGGACCCAATGTGGACTTATTCCAAAGCGAGGCGGGCACACCAAGCGAGCCATTTGGGC

Reverse complement sequence

GCCCAAATGGCTCGCTTGGTGTGCCCGCCTCGCTTTGGAATAAGTCCACATTGGGTCCCTGTAACATCCTGAAAATTCCCAATAATAAAAATCACTAAAA[TTTTGAAC/TTTTGAAT,C]
TTTTTAAAACTGTTGCATCATGCTGGTTGTTATGATTGATATTGCTTGCCAAACCGTAAATAATCACAAAGAAAGTAAAGAAAAGATCGACATTTAAGCA

Allele Frequencies:

Populations	Population Size	Frequency of GTTCAAAA(primary allele)	Frequency of ATTCAAAA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.00%	32.40%	0.49%	0.00%	G: 0.08%
All Indica	2759	44.50%	54.80%	0.62%	0.00%	G: 0.04%
All Japonica	1512	99.70%	0.10%	0.13%	0.00%	NA
Aus	269	98.50%	0.00%	0.37%	0.00%	G: 1.12%
Indica I	595	19.70%	79.70%	0.67%	0.00%	NA
Indica II	465	80.00%	19.80%	0.22%	0.00%	NA
Indica III	913	38.00%	61.60%	0.44%	0.00%	NA
Indica Intermediate	786	49.90%	49.00%	1.02%	0.00%	G: 0.13%
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	78.90%	17.80%	3.33%	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
vg0427444019	GTTCAAAA -> G	LOC_Os04g46310.1	upstream_gene_variant ; 442.0bp to feature; MODIFIER	silent_mutation	Average:95.684; most accessible tissue: Callus, score: 97.082	N	N	N	N
vg0427444019	GTTCAAAA -> G	LOC_Os04g46300-LOC_Os04g46310	intergenic_region ; MODIFIER	silent_mutation	Average:95.684; most accessible tissue: Callus, score: 97.082	N	N	N	N
vg0427444019	GTTCAAAA -> ATTCAAAA	LOC_Os04g46310.1	upstream_gene_variant ; 443.0bp to feature; MODIFIER	silent_mutation	Average:95.684; most accessible tissue: Callus, score: 97.082	N	N	N	N
vg0427444019	GTTCAAAA -> ATTCAAAA	LOC_Os04g46300-LOC_Os04g46310	intergenic_region ; MODIFIER	silent_mutation	Average:95.684; most accessible tissue: Callus, score: 97.082	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)
vg0427444019	GTTCA*	ATTCA*	-0.01	-0.01	-0.02	-0.01	-0.02	-0.02
vg0427444019	GTTCA*	G	0.07	0.02	0.09	0.06	0.08	0.09

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427444019	NA	1.26E-08	mr1174	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
vg0427444019	NA	7.25E-12	mr1174_2	Ind_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
vg0427444019	NA	1.65E-10	mr1347_2	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
vg0427444019	NA	8.02E-06	mr1355_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
vg0427444019	NA	5.40E-06	mr1923_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