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Detailed information for vg0916049005:

Variant ID: vg0916049005 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 16049005
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GAAAAGTCCCGGGTACCTAAATTTGTCCCGAAATAATGTGGCCGAGCTGGCGGGCGGTAAATACCCACCCCGTTTTCACCCCTATGCTATGGTTTCCAAG[C/A]
CATCCAAATTGCCATGGGACCTATATTGCACCGGTTTTAATAGTTGAGAGACCCGTTGAATGTGGTGTTTCGGTTGAAAGACGAAAATCAGATTTGTTGA

Reverse complement sequence

TCAACAAATCTGATTTTCGTCTTTCAACCGAAACACCACATTCAACGGGTCTCTCAACTATTAAAACCGGTGCAATATAGGTCCCATGGCAATTTGGATG[G/T]
CTTGGAAACCATAGCATAGGGGTGAAAACGGGGTGGGTATTTACCGCCCGCCAGCTCGGCCACATTATTTCGGGACAAATTTAGGTACCCGGGACTTTTC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.60%	0.70%	0.63%	51.99%	NA
All Indica	2759	18.80%	0.00%	0.76%	80.43%	NA
All Japonica	1512	96.70%	2.20%	0.46%	0.66%	NA
Aus	269	26.00%	0.00%	0.37%	73.61%	NA
Indica I	595	40.30%	0.00%	0.50%	59.16%	NA
Indica II	465	12.90%	0.00%	0.43%	86.67%	NA
Indica III	913	5.60%	0.10%	0.88%	93.43%	NA
Indica Intermediate	786	21.20%	0.00%	1.02%	77.74%	NA
Temperate Japonica	767	99.30%	0.00%	0.26%	0.39%	NA
Tropical Japonica	504	91.70%	6.30%	0.79%	1.19%	NA
Japonica Intermediate	241	98.80%	0.40%	0.41%	0.41%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	66.70%	1.10%	1.11%	31.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0916049005	C -> DEL	N	N	silent_mutation	Average:91.602; most accessible tissue: Callus, score: 97.226	N	N	N	N
vg0916049005	C -> A	LOC_Os09g26540.1	upstream_gene_variant ; 3538.0bp to feature; MODIFIER	silent_mutation	Average:91.602; most accessible tissue: Callus, score: 97.226	N	N	N	N
vg0916049005	C -> A	LOC_Os09g26550.2	upstream_gene_variant ; 133.0bp to feature; MODIFIER	silent_mutation	Average:91.602; most accessible tissue: Callus, score: 97.226	N	N	N	N
vg0916049005	C -> A	LOC_Os09g26540.2	upstream_gene_variant ; 3538.0bp to feature; MODIFIER	silent_mutation	Average:91.602; most accessible tissue: Callus, score: 97.226	N	N	N	N
vg0916049005	C -> A	LOC_Os09g26540-LOC_Os09g26550	intergenic_region ; MODIFIER	silent_mutation	Average:91.602; most accessible tissue: Callus, score: 97.226	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)
vg0916049005	C	A	-0.01	-0.02	-0.02	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0916049005	6.92E-06	1.40E-07	mr1220_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
vg0916049005	3.94E-06	3.93E-06	mr1574_2	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
vg0916049005	NA	2.48E-06	mr1786_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
vg0916049005	NA	1.62E-08	mr1800_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
vg0916049005	3.64E-06	NA	mr1849_2	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