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Detailed information for vg0906912896:

Variant ID: vg0906912896 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6912896
Reference Allele: C	Alternative Allele: T,A,G
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TCATCACTAAGCATATCATACATAATCAAGAGCAGCCCCAAAATGCAGTACATATGTGATGGATGGCGGCATGTTCTATGTTGCGTGCTGACTGTAAGGG[C/T,A,G]
AATCCTAACCCATGGTGTCTATAGATAGTGTCTAGACAACAGAAACAATAATAAATGTATGTAGACACTACCTCTCCAATGCATAGTGTCTATAGCAGTT

Reverse complement sequence

AACTGCTATAGACACTATGCATTGGAGAGGTAGTGTCTACATACATTTATTATTGTTTCTGTTGTCTAGACACTATCTATAGACACCATGGGTTAGGATT[G/A,T,C]
CCCTTACAGTCAGCACGCAACATAGAACATGCCGCCATCCATCACATATGTACTGCATTTTGGGGCTGCTCTTGATTATGTATGATATGCTTAGTGATGA

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	97.40%	2.40%	0.06%	0.00%	G: 0.06%; A: 0.02%
All Indica	2759	99.90%	0.00%	0.00%	0.00%	G: 0.11%
All Japonica	1512	92.30%	7.50%	0.20%	0.00%	A: 0.07%
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.00%	0.00%	G: 0.11%
Indica Intermediate	786	99.70%	0.00%	0.00%	0.00%	G: 0.25%
Temperate Japonica	767	99.60%	0.10%	0.26%	0.00%	NA
Tropical Japonica	504	78.20%	21.40%	0.20%	0.00%	A: 0.20%
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0906912896	C -> G	LOC_Os09g12200-LOC_Os09g12210	intergenic_region ; MODIFIER	silent_mutation	Average:74.089; most accessible tissue: Zhenshan97 panicle, score: 91.845	N	N	N	N
vg0906912896	C -> T	LOC_Os09g12200-LOC_Os09g12210	intergenic_region ; MODIFIER	silent_mutation	Average:74.089; most accessible tissue: Zhenshan97 panicle, score: 91.845	N	N	N	N
vg0906912896	C -> A	LOC_Os09g12200-LOC_Os09g12210	intergenic_region ; MODIFIER	silent_mutation	Average:74.089; most accessible tissue: Zhenshan97 panicle, score: 91.845	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)
vg0906912896	C	A	-0.04	-0.03	-0.02	-0.1	-0.07	-0.07
vg0906912896	C	G	-0.02	-0.01	-0.02	-0.07	-0.04	-0.02
vg0906912896	C	T	-0.02	-0.01	-0.01	-0.05	-0.07	-0.09

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906912896	NA	6.24E-06	mr1304	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
vg0906912896	NA	1.96E-07	mr1364	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
vg0906912896	NA	6.56E-08	mr1443	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
vg0906912896	NA	6.70E-07	mr1925	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
vg0906912896	3.88E-07	3.88E-07	mr1076_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
vg0906912896	NA	1.37E-07	mr1083_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
vg0906912896	NA	9.47E-06	mr1226_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
vg0906912896	NA	1.68E-10	mr1364_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
vg0906912896	NA	3.14E-06	mr1408_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
vg0906912896	NA	7.22E-07	mr1498_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
vg0906912896	NA	1.10E-07	mr1653_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
vg0906912896	NA	9.12E-06	mr1707_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
vg0906912896	4.45E-06	4.45E-06	mr1846_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