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Detailed information for vg0921374490:

Variant ID: vg0921374490 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 21374490
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGTTAAGAGGCTCATATCAACGCGAAAAATACAATTTCACACTTTCACATCCCTTATCTTTTCTCGCAGAGGTACTCCTTCCATCCTAAAATGTAGTAA[C/A]
CTAAGATATGTTTAGTTTTATAGTCCTAGGATGTCTCAGCTCGTACTATATTGCTATATTTTGGGATAAAGGCAGTACTCGATGCCGTCGTTTTCTTTTC

Reverse complement sequence

GAAAAGAAAACGACGGCATCGAGTACTGCCTTTATCCCAAAATATAGCAATATAGTACGAGCTGAGACATCCTAGGACTATAAAACTAAACATATCTTAG[G/T]
TTACTACATTTTAGGATGGAAGGAGTACCTCTGCGAGAAAAGATAAGGGATGTGAAAGTGTGAAATTGTATTTTTCGCGTTGATATGAGCCTCTTAACAT

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	96.30%	3.50%	0.17%	0.00%	NA
All Indica	2759	93.70%	6.00%	0.29%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	93.30%	6.20%	0.43%	0.00%	NA
Indica III	913	92.80%	7.20%	0.00%	0.00%	NA
Indica Intermediate	786	92.20%	7.00%	0.76%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0921374490	C -> A	LOC_Os09g37050.1	upstream_gene_variant ; 2114.0bp to feature; MODIFIER	silent_mutation	Average:68.107; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg0921374490	C -> A	LOC_Os09g37040.1	downstream_gene_variant ; 4097.0bp to feature; MODIFIER	silent_mutation	Average:68.107; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg0921374490	C -> A	LOC_Os09g37060.1	downstream_gene_variant ; 1323.0bp to feature; MODIFIER	silent_mutation	Average:68.107; most accessible tissue: Zhenshan97 panicle, score: 92.133	N	N	N	N
vg0921374490	C -> A	LOC_Os09g37050-LOC_Os09g37060	intergenic_region ; MODIFIER	silent_mutation	Average:68.107; most accessible tissue: Zhenshan97 panicle, score: 92.133	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)
vg0921374490	C	A	0.03	0.01	0.02	0.0	0.03	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0921374490	NA	4.17E-06	mr1004	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
vg0921374490	NA	5.80E-06	mr1005	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
vg0921374490	3.05E-09	3.71E-13	mr1006	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
vg0921374490	1.74E-07	2.47E-10	mr1007	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
vg0921374490	4.84E-09	1.13E-13	mr1052	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
vg0921374490	NA	2.24E-06	mr1004_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
vg0921374490	8.58E-09	1.13E-13	mr1006_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
vg0921374490	NA	5.44E-06	mr1008_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