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Detailed information for vg0701510236:

Variant ID: vg0701510236 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 1510236
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GCCAGCGGGTAATAGTAGAGAATGTCCTCATCATACAATATGAGAAAAATGGATTATTACTTAATTAATTAACAAACGCTAGAAATCACAACGTACTCGA[T/C]
AGAATAAAAAAAAATATGTGTTAGGACATGAGGCATATCATACCATCGAGTACGTGTATATACTTTTGTGCATGCATCCGTTAACCTATGCGTGTATGTG

Reverse complement sequence

CACATACACGCATAGGTTAACGGATGCATGCACAAAAGTATATACACGTACTCGATGGTATGATATGCCTCATGTCCTAACACATATTTTTTTTTATTCT[A/G]
TCGAGTACGTTGTGATTTCTAGCGTTTGTTAATTAATTAAGTAATAATCCATTTTTCTCATATTGTATGATGAGGACATTCTCTACTATTACCCGCTGGC

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	86.10%	13.90%	0.02%	0.00%	NA
All Indica	2759	82.30%	17.70%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	40.10%	59.90%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	70.30%	29.70%	0.00%	0.00%	NA
Indica III	913	82.40%	17.60%	0.00%	0.00%	NA
Indica Intermediate	786	76.30%	23.50%	0.13%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0701510236	T -> C	LOC_Os07g03710.1	upstream_gene_variant ; 1789.0bp to feature; MODIFIER	silent_mutation	Average:71.382; most accessible tissue: Minghui63 root, score: 92.181	N	N	N	N
vg0701510236	T -> C	LOC_Os07g03700-LOC_Os07g03710	intergenic_region ; MODIFIER	silent_mutation	Average:71.382; most accessible tissue: Minghui63 root, score: 92.181	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)
vg0701510236	T	C	0.04	0.0	0.0	0.0	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0701510236	1.85E-06	NA	Heading_date	Ind_All	YES	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
vg0701510236	NA	2.03E-06	mr1174	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
vg0701510236	NA	1.14E-06	mr1188	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
vg0701510236	NA	4.35E-07	mr1188_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
vg0701510236	NA	6.27E-10	mr1510_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
vg0701510236	NA	3.20E-07	mr1691_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
vg0701510236	NA	4.24E-07	mr1702_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