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Detailed information for vg0801556836:

Variant ID: vg0801556836 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 1556836
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAGAGGTCTGCACCTCCCAAAAGTCAGCAAAGATGGCCACGCCTGATAATTCAGATTCAGAGTCAAGGAGGAGGAGTACAACTCTACTCAACTTGCTGTT[T/C]
ATGACAGTGACTTGTTTAATTCGCTCGTTTTCCTTAAAGTGGGATCAACTTAAATTTAGAGTTGATTTTTGTTTTTTTTATCGTAGTTTATTTTTCAGCC

Reverse complement sequence

GGCTGAAAAATAAACTACGATAAAAAAAACAAAAATCAACTCTAAATTTAAGTTGATCCCACTTTAAGGAAAACGAGCGAATTAAACAAGTCACTGTCAT[A/G]
AACAGCAAGTTGAGTAGAGTTGTACTCCTCCTCCTTGACTCTGAATCTGAATTATCAGGCGTGGCCATCTTTGCTGACTTTTGGGAGGTGCAGACCTCTG

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%	48.60%	0.19%	0.00%	NA
All Indica	2759	19.10%	80.70%	0.25%	0.00%	NA
All Japonica	1512	97.80%	2.20%	0.00%	0.00%	NA
Aus	269	98.90%	1.10%	0.00%	0.00%	NA
Indica I	595	7.20%	92.60%	0.17%	0.00%	NA
Indica II	465	4.90%	94.80%	0.22%	0.00%	NA
Indica III	913	28.90%	71.00%	0.11%	0.00%	NA
Indica Intermediate	786	24.90%	74.60%	0.51%	0.00%	NA
Temperate Japonica	767	96.90%	3.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	63.30%	34.40%	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
vg0801556836	T -> C	LOC_Os08g03350.1	upstream_gene_variant ; 4918.0bp to feature; MODIFIER	silent_mutation	Average:91.01; most accessible tissue: Zhenshan97 root, score: 98.685	N	N	N	N
vg0801556836	T -> C	LOC_Os08g03330-LOC_Os08g03350	intergenic_region ; MODIFIER	silent_mutation	Average:91.01; most accessible tissue: Zhenshan97 root, score: 98.685	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)
vg0801556836	T	C	0.09	0.05	0.02	-0.02	0.03	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0801556836	NA	5.58E-26	mr1003	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
vg0801556836	NA	5.02E-06	mr1003	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
vg0801556836	NA	3.36E-25	mr1051	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
vg0801556836	NA	9.82E-18	mr1255	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
vg0801556836	NA	1.05E-14	mr1261	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
vg0801556836	NA	1.34E-09	mr1352	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
vg0801556836	NA	3.47E-30	mr1051_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
vg0801556836	NA	4.12E-07	mr1051_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
vg0801556836	NA	2.55E-22	mr1877_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