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Detailed information for vg1009498741:

Variant ID: vg1009498741 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 9498741
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GACCAAAGGTTGAGATTCATGGAGCATATGAACTTTGGTTCATATATGCTTAGACCTATATGTACGTGTGTGTATATAGAGAGTAGCTCTATTATACACC[C/T]
CTTCCTTAGAATAACTATTCTACGCCCCTCTCCCACCTTCCATCTGTCCCTCCCGAAGTCTCAATCTCTCATCCCCCAATCTCTCCTTTTCTTCTTTTTT

Reverse complement sequence

AAAAAAGAAGAAAAGGAGAGATTGGGGGATGAGAGATTGAGACTTCGGGAGGGACAGATGGAAGGTGGGAGAGGGGCGTAGAATAGTTATTCTAAGGAAG[G/A]
GGTGTATAATAGAGCTACTCTCTATATACACACACGTACATATAGGTCTAAGCATATATGAACCAAAGTTCATATGCTCCATGAATCTCAACCTTTGGTC

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	51.20%	29.50%	3.89%	15.40%	NA
All Indica	2759	67.50%	11.90%	6.31%	14.28%	NA
All Japonica	1512	13.40%	65.40%	0.53%	20.70%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	85.40%	2.50%	5.21%	6.89%	NA
Indica II	465	74.20%	8.80%	5.16%	11.83%	NA
Indica III	913	48.70%	22.70%	7.23%	21.36%	NA
Indica Intermediate	786	71.80%	8.40%	6.74%	13.10%	NA
Temperate Japonica	767	1.30%	83.20%	0.26%	15.25%	NA
Tropical Japonica	504	32.70%	47.60%	0.60%	19.05%	NA
Japonica Intermediate	241	11.20%	46.10%	1.24%	41.49%	NA
VI/Aromatic	96	44.80%	40.60%	0.00%	14.58%	NA
Intermediate	90	50.00%	41.10%	1.11%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1009498741	C -> T	LOC_Os10g18700.1	upstream_gene_variant ; 3057.0bp to feature; MODIFIER	silent_mutation	Average:53.729; most accessible tissue: Zhenshan97 root, score: 91.073	N	N	N	N
vg1009498741	C -> T	LOC_Os10g18670-LOC_Os10g18700	intergenic_region ; MODIFIER	silent_mutation	Average:53.729; most accessible tissue: Zhenshan97 root, score: 91.073	N	N	N	N
vg1009498741	C -> DEL	N	N	silent_mutation	Average:53.729; most accessible tissue: Zhenshan97 root, score: 91.073	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)
vg1009498741	C	T	0.02	0.01	0.06	-0.04	0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1009498741	NA	1.08E-25	mr1238	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
vg1009498741	NA	1.87E-16	mr1484	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
vg1009498741	NA	7.75E-23	mr1841	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
vg1009498741	NA	3.16E-14	mr1900	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
vg1009498741	NA	5.80E-09	mr1986	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
vg1009498741	NA	9.79E-20	mr1900_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
vg1009498741	NA	4.56E-18	mr1945_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