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Detailed information for vg0134802811:

Variant ID: vg0134802811 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34802811
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

TGCAGCCTGCAAATGAGGTCGTGTGTGTGCCGCCCTTGCTTTCTTTTGTTCTTTGCATGTGCTTGCGAGCTGGGTCTTTTGCGTCACTGCGTGTGAGGCG[T/C]
CTGCCAATTGGTTATCATCAGTAGCATCTCACCGTTGACAGCTTACAGAAATCAGAGGTTCTTGCGAGGTCTGGCCGTCTGGATGAAGTACTCCTAGTTC

Reverse complement sequence

GAACTAGGAGTACTTCATCCAGACGGCCAGACCTCGCAAGAACCTCTGATTTCTGTAAGCTGTCAACGGTGAGATGCTACTGATGATAACCAATTGGCAG[A/G]
CGCCTCACACGCAGTGACGCAAAAGACCCAGCTCGCAAGCACATGCAAAGAACAAAAGAAAGCAAGGGCGGCACACACACGACCTCATTTGCAGGCTGCA

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	94.60%	5.30%	0.11%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.00%	0.00%	NA
All Japonica	1512	85.10%	14.60%	0.33%	0.00%	NA
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	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	93.50%	6.40%	0.13%	0.00%	NA
Tropical Japonica	504	75.80%	23.80%	0.40%	0.00%	NA
Japonica Intermediate	241	77.60%	21.60%	0.83%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0134802811	T -> C	LOC_Os01g60190.1	upstream_gene_variant ; 1473.0bp to feature; MODIFIER	silent_mutation	Average:95.18; most accessible tissue: Zhenshan97 flower, score: 99.61	N	N	N	N
vg0134802811	T -> C	LOC_Os01g60190.2	upstream_gene_variant ; 1568.0bp to feature; MODIFIER	silent_mutation	Average:95.18; most accessible tissue: Zhenshan97 flower, score: 99.61	N	N	N	N
vg0134802811	T -> C	LOC_Os01g60160.1	downstream_gene_variant ; 1983.0bp to feature; MODIFIER	silent_mutation	Average:95.18; most accessible tissue: Zhenshan97 flower, score: 99.61	N	N	N	N
vg0134802811	T -> C	LOC_Os01g60170.1	downstream_gene_variant ; 550.0bp to feature; MODIFIER	silent_mutation	Average:95.18; most accessible tissue: Zhenshan97 flower, score: 99.61	N	N	N	N
vg0134802811	T -> C	LOC_Os01g60180.1	downstream_gene_variant ; 681.0bp to feature; MODIFIER	silent_mutation	Average:95.18; most accessible tissue: Zhenshan97 flower, score: 99.61	N	N	N	N
vg0134802811	T -> C	LOC_Os01g60170-LOC_Os01g60180	intergenic_region ; MODIFIER	silent_mutation	Average:95.18; most accessible tissue: Zhenshan97 flower, score: 99.61	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)
vg0134802811	T	C	-0.01	-0.04	-0.04	0.0	-0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134802811	3.01E-06	NA	mr1018	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
vg0134802811	1.85E-06	NA	mr1489	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
vg0134802811	3.13E-07	NA	mr1778	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
vg0134802811	1.13E-06	NA	mr1023_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
vg0134802811	8.73E-07	2.83E-09	mr1289_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
vg0134802811	NA	8.60E-06	mr1419_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
vg0134802811	NA	2.32E-06	mr1467_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
vg0134802811	2.55E-07	NA	mr1489_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
vg0134802811	NA	2.45E-06	mr1556_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
vg0134802811	NA	6.35E-07	mr1604_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
vg0134802811	NA	2.95E-06	mr1687_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
vg0134802811	NA	2.32E-06	mr1764_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
vg0134802811	1.71E-07	NA	mr1778_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
vg0134802811	NA	3.14E-07	mr1824_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