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Detailed information for vg0920070140:

Variant ID: vg0920070140 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 20070140
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.63, C: 0.37, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

CCTAATTGATACAACTAAGCAAACAACCGCTCTTGCTCCTGCACATCCTAGCTATGGTCAGCTTGGATGCCTCATATGGGACATATTAGAGGGACTCAAG[T/C]
AAACAAACAGACTCGTAGTGCAGGGCCATATGAAATGAGTGGTGCAAGACAAATCAAGAGCTTGTATGTTAAAAGTACATGTGTGTTCGTGTGTTATGGT

Reverse complement sequence

ACCATAACACACGAACACACATGTACTTTTAACATACAAGCTCTTGATTTGTCTTGCACCACTCATTTCATATGGCCCTGCACTACGAGTCTGTTTGTTT[A/G]
CTTGAGTCCCTCTAATATGTCCCATATGAGGCATCCAAGCTGACCATAGCTAGGATGTGCAGGAGCAAGAGCGGTTGTTTGCTTAGTTGTATCAATTAGG

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	51.10%	48.70%	0.21%	0.02%	NA
All Indica	2759	85.00%	14.80%	0.22%	0.00%	NA
All Japonica	1512	0.10%	99.70%	0.07%	0.07%	NA
Aus	269	11.20%	88.80%	0.00%	0.00%	NA
Indica I	595	89.20%	10.60%	0.17%	0.00%	NA
Indica II	465	85.80%	13.80%	0.43%	0.00%	NA
Indica III	913	88.40%	11.50%	0.11%	0.00%	NA
Indica Intermediate	786	77.50%	22.30%	0.25%	0.00%	NA
Temperate Japonica	767	0.10%	99.70%	0.13%	0.00%	NA
Tropical Japonica	504	0.00%	100.00%	0.00%	0.00%	NA
Japonica Intermediate	241	0.40%	99.20%	0.00%	0.41%	NA
VI/Aromatic	96	17.70%	82.30%	0.00%	0.00%	NA
Intermediate	90	20.00%	76.70%	3.33%	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
vg0920070140	T -> DEL	N	N	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g33986.1	upstream_gene_variant ; 627.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g34000.1	upstream_gene_variant ; 3675.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g33986.2	upstream_gene_variant ; 782.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g34000.4	upstream_gene_variant ; 3670.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g34000.2	upstream_gene_variant ; 3676.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g34000.3	upstream_gene_variant ; 3676.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g33980.1	downstream_gene_variant ; 3526.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g33992.1	downstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g33992.2	downstream_gene_variant ; 383.0bp to feature; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	N	N	N	N
vg0920070140	T -> C	LOC_Os09g33986-LOC_Os09g33992	intergenic_region ; MODIFIER	silent_mutation	Average:74.538; most accessible tissue: Zhenshan97 flag leaf, score: 88.022	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)
vg0920070140	T	C	0.0	0.01	0.02	0.02	0.08	0.13

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0920070140	NA	6.40E-09	mr1047	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
vg0920070140	NA	1.81E-10	mr1151	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
vg0920070140	NA	1.43E-15	mr1165	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
vg0920070140	NA	2.70E-11	mr1172	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
vg0920070140	1.01E-25	3.29E-19	mr1216	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
vg0920070140	5.34E-22	5.98E-33	mr1216	Ind_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
vg0920070140	NA	3.21E-11	mr1325	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
vg0920070140	NA	1.60E-13	mr1326	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
vg0920070140	NA	4.92E-07	mr1532	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
vg0920070140	NA	3.49E-13	mr1744	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
vg0920070140	NA	5.77E-31	mr1793	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
vg0920070140	NA	2.16E-07	mr1796	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
vg0920070140	NA	3.81E-07	mr1990	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
vg0920070140	NA	1.70E-06	mr1158_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
vg0920070140	6.32E-06	NA	mr1216_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
vg0920070140	NA	4.36E-06	mr1380_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
vg0920070140	2.07E-06	4.65E-51	mr1793_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
vg0920070140	NA	8.30E-07	mr1793_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