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Detailed information for vg1003397297:

Variant ID: vg1003397297 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3397297
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.04, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTATGGTAGAACTGTAAGGTGGTAGATAGGTGTTGCCGACAAGGTCGATTTGACGAGGACCTCCGGGCTAGCCGATGTGAAAAATCTGCCCTTCCAAC[T/C]
CGGTATTCTCAATCTTATCTTATCCACTAACGGTTGTAGATCAACTTTCATCAGTTTTATGGTGTGAAGCAGCAAACTGAGATATTTGCGAGGGAATGAC

Reverse complement sequence

GTCATTCCCTCGCAAATATCTCAGTTTGCTGCTTCACACCATAAAACTGATGAAAGTTGATCTACAACCGTTAGTGGATAAGATAAGATTGAGAATACCG[A/G]
GTTGGAAGGGCAGATTTTTCACATCGGCTAGCCCGGAGGTCCTCGTCAAATCGACCTTGTCGGCAACACCTATCTACCACCTTACAGTTCTACCATAGAA

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	75.20%	24.40%	0.36%	0.13%	NA
All Indica	2759	60.70%	38.50%	0.58%	0.22%	NA
All Japonica	1512	97.40%	2.60%	0.00%	0.00%	NA
Aus	269	96.70%	3.30%	0.00%	0.00%	NA
Indica I	595	55.10%	43.50%	1.18%	0.17%	NA
Indica II	465	74.20%	24.30%	0.65%	0.86%	NA
Indica III	913	49.90%	49.70%	0.33%	0.00%	NA
Indica Intermediate	786	69.60%	29.90%	0.38%	0.13%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	93.30%	6.70%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	72.90%	27.10%	0.00%	0.00%	NA
Intermediate	90	81.10%	17.80%	1.11%	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
vg1003397297	T -> C	LOC_Os10g06580.1	upstream_gene_variant ; 2283.0bp to feature; MODIFIER	silent_mutation	Average:88.641; most accessible tissue: Callus, score: 97.641	N	N	N	N
vg1003397297	T -> C	LOC_Os10g06600.1	downstream_gene_variant ; 502.0bp to feature; MODIFIER	silent_mutation	Average:88.641; most accessible tissue: Callus, score: 97.641	N	N	N	N
vg1003397297	T -> C	LOC_Os10g06580-LOC_Os10g06600	intergenic_region ; MODIFIER	silent_mutation	Average:88.641; most accessible tissue: Callus, score: 97.641	N	N	N	N
vg1003397297	T -> DEL	N	N	silent_mutation	Average:88.641; most accessible tissue: Callus, score: 97.641	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)
vg1003397297	T	C	0.03	0.03	0.02	0.04	0.03	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003397297	2.01E-10	NA	mr1538	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
vg1003397297	2.92E-10	9.71E-13	mr1538	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
vg1003397297	1.08E-17	2.00E-22	mr1547	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
vg1003397297	9.27E-16	7.50E-22	mr1547	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
vg1003397297	8.82E-48	2.42E-57	mr1709	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
vg1003397297	2.48E-44	2.94E-71	mr1709	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
vg1003397297	1.38E-13	NA	mr1538_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
vg1003397297	6.11E-14	1.09E-20	mr1538_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
vg1003397297	1.48E-21	5.64E-27	mr1547_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
vg1003397297	3.76E-21	2.07E-29	mr1547_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
vg1003397297	6.82E-70	2.16E-99	mr1709_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
vg1003397297	5.27E-59	1.85E-112	mr1709_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