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Detailed information for vg0334733257:

Variant ID: vg0334733257 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 34733257
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTTGCAAACAGACTGAAGTTATCTCCGTACACGTACGCGCAAGGAAGAGACTGGTGGACCCAAAAGGCCCTCCGTGGGAGAGATAGGCTTAACGAGGC[T/C]
CAAATACACCTAATTAGGCTCAATTGGACCCATCCTAAACGAGCCCCCTAATTAGTATCCTTAGCGAATACATGGCTCCCATGAGTTGAATGGTGAAATT

Reverse complement sequence

AATTTCACCATTCAACTCATGGGAGCCATGTATTCGCTAAGGATACTAATTAGGGGGCTCGTTTAGGATGGGTCCAATTGAGCCTAATTAGGTGTATTTG[A/G]
GCCTCGTTAAGCCTATCTCTCCCACGGAGGGCCTTTTGGGTCCACCAGTCTCTTCCTTGCGCGTACGTGTACGGAGATAACTTCAGTCTGTTTGCAAAGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	84.00%	14.50%	1.48%	0.00%	NA
All Indica	2759	99.30%	0.50%	0.14%	0.00%	NA
All Japonica	1512	52.40%	43.70%	3.97%	0.00%	NA
Aus	269	97.40%	1.10%	1.49%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	98.30%	1.50%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.80%	0.25%	0.00%	NA
Temperate Japonica	767	29.30%	65.60%	5.08%	0.00%	NA
Tropical Japonica	504	82.90%	15.50%	1.59%	0.00%	NA
Japonica Intermediate	241	61.80%	32.80%	5.39%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	10.00%	2.22%	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
vg0334733257	T -> C	LOC_Os03g61140.1	upstream_gene_variant ; 1724.0bp to feature; MODIFIER	silent_mutation	Average:96.461; most accessible tissue: Minghui63 panicle, score: 99.057	N	N	N	N
vg0334733257	T -> C	LOC_Os03g61140.2	upstream_gene_variant ; 1726.0bp to feature; MODIFIER	silent_mutation	Average:96.461; most accessible tissue: Minghui63 panicle, score: 99.057	N	N	N	N
vg0334733257	T -> C	LOC_Os03g61150.1	downstream_gene_variant ; 196.0bp to feature; MODIFIER	silent_mutation	Average:96.461; most accessible tissue: Minghui63 panicle, score: 99.057	N	N	N	N
vg0334733257	T -> C	LOC_Os03g61150.2	downstream_gene_variant ; 196.0bp to feature; MODIFIER	silent_mutation	Average:96.461; most accessible tissue: Minghui63 panicle, score: 99.057	N	N	N	N
vg0334733257	T -> C	LOC_Os03g61150.3	downstream_gene_variant ; 214.0bp to feature; MODIFIER	silent_mutation	Average:96.461; most accessible tissue: Minghui63 panicle, score: 99.057	N	N	N	N
vg0334733257	T -> C	LOC_Os03g61140-LOC_Os03g61150	intergenic_region ; MODIFIER	silent_mutation	Average:96.461; most accessible tissue: Minghui63 panicle, score: 99.057	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)
vg0334733257	T	C	0.25	0.46	0.45	0.34	0.2	0.17

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0334733257	NA	3.16E-10	Heading_date	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0334733257	NA	3.23E-15	Plant_height	Jap_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0334733257	NA	4.53E-14	Spikelet_length	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0334733257	NA	2.41E-08	mr1002	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
vg0334733257	NA	2.20E-06	mr1002	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
vg0334733257	2.30E-07	NA	mr1024	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
vg0334733257	NA	1.18E-12	mr1940	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
vg0334733257	3.15E-06	7.60E-14	mr1002_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
vg0334733257	NA	1.51E-10	mr1002_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
vg0334733257	3.30E-06	3.30E-06	mr1616_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
vg0334733257	NA	5.95E-06	mr1647_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
vg0334733257	NA	6.27E-07	mr1648_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
vg0334733257	NA	3.91E-09	mr1794_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
vg0334733257	NA	1.81E-08	mr1805_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
vg0334733257	NA	2.91E-06	mr1851_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
vg0334733257	NA	1.64E-08	mr1940_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