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Detailed information for vg0117911485:

Variant ID: vg0117911485 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17911485
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

TAATGTAGCATCACATATGCTAATCATGAATTAATTAGGCTCAATATATTCGTCTCGTGAATTAGTTTAGGATTATGAAATGGGTTTTGTTATTAGTCTA[T/C]
ATTTAATACTTCTAATTAGTGTCTAAACATCCGATGTGATAGGACCTGAATTCAAACTCATTTGTGGCGAGAAAGTTCAATTATTCAACGAAACACCAAA

Reverse complement sequence

TTTGGTGTTTCGTTGAATAATTGAACTTTCTCGCCACAAATGAGTTTGAATTCAGGTCCTATCACATCGGATGTTTAGACACTAATTAGAAGTATTAAAT[A/G]
TAGACTAATAACAAAACCCATTTCATAATCCTAAACTAATTCACGAGACGAATATATTGAGCCTAATTAATTCATGATTAGCATATGTGATGCTACATTA

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	63.50%	36.30%	0.23%	0.00%	NA
All Indica	2759	97.70%	2.10%	0.25%	0.00%	NA
All Japonica	1512	4.40%	95.50%	0.07%	0.00%	NA
Aus	269	70.30%	29.70%	0.00%	0.00%	NA
Indica I	595	99.50%	0.30%	0.17%	0.00%	NA
Indica II	465	96.30%	3.40%	0.22%	0.00%	NA
Indica III	913	99.20%	0.50%	0.22%	0.00%	NA
Indica Intermediate	786	95.30%	4.30%	0.38%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	6.20%	93.70%	0.20%	0.00%	NA
Japonica Intermediate	241	10.80%	89.20%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	47.80%	48.90%	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
vg0117911485	T -> C	LOC_Os01g32660.1	downstream_gene_variant ; 1326.0bp to feature; MODIFIER	silent_mutation	Average:80.415; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	N	N	N	N
vg0117911485	T -> C	LOC_Os01g32670.1	downstream_gene_variant ; 38.0bp to feature; MODIFIER	silent_mutation	Average:80.415; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	N	N	N	N
vg0117911485	T -> C	LOC_Os01g32660.3	downstream_gene_variant ; 3763.0bp to feature; MODIFIER	silent_mutation	Average:80.415; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	N	N	N	N
vg0117911485	T -> C	LOC_Os01g32660.2	downstream_gene_variant ; 1326.0bp to feature; MODIFIER	silent_mutation	Average:80.415; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	N	N	N	N
vg0117911485	T -> C	LOC_Os01g32660.4	downstream_gene_variant ; 1326.0bp to feature; MODIFIER	silent_mutation	Average:80.415; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	N	N	N	N
vg0117911485	T -> C	LOC_Os01g32660.5	downstream_gene_variant ; 1311.0bp to feature; MODIFIER	silent_mutation	Average:80.415; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	N	N	N	N
vg0117911485	T -> C	LOC_Os01g32660-LOC_Os01g32670	intergenic_region ; MODIFIER	silent_mutation	Average:80.415; most accessible tissue: Zhenshan97 flag leaf, score: 90.181	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)
vg0117911485	T	C	-0.01	-0.01	-0.01	-0.01	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117911485	NA	4.36E-16	mr1228	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
vg0117911485	NA	5.47E-29	mr1298	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
vg0117911485	NA	4.70E-54	mr1519	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
vg0117911485	NA	1.21E-20	mr1698	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
vg0117911485	NA	3.09E-24	mr1731	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
vg0117911485	NA	1.36E-70	mr1087_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
vg0117911485	NA	8.37E-54	mr1200_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
vg0117911485	NA	2.79E-17	mr1281_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
vg0117911485	NA	8.55E-10	mr1398_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
vg0117911485	2.60E-08	2.76E-56	mr1519_2	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
vg0117911485	NA	1.85E-07	mr1568_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
vg0117911485	NA	3.77E-21	mr1698_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
vg0117911485	NA	2.32E-23	mr1708_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
vg0117911485	NA	4.11E-13	mr1717_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
vg0117911485	NA	1.03E-06	mr1727_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
vg0117911485	NA	6.87E-14	mr1770_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
vg0117911485	NA	2.54E-47	mr1861_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
vg0117911485	NA	1.65E-24	mr1916_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