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Detailed information for vg1119375381:

Variant ID: vg1119375381 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19375381
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGGTGCACATACATAATCCGTTGAATTGAACGACGGAATGCTGTCCCGAACGACGACACCTCACACTCGGTAACACACGACACCACCTAGAAGTTGTC[A/G]
TCTATCTGACTAACATAGTCATTGATCTATGAATATATTAATACACTCGTCATCGCCGATCTTATGGATCAGCACGTTTGGGACACTGTTGGTTGTGACT

Reverse complement sequence

AGTCACAACCAACAGTGTCCCAAACGTGCTGATCCATAAGATCGGCGATGACGAGTGTATTAATATATTCATAGATCAATGACTATGTTAGTCAGATAGA[T/C]
GACAACTTCTAGGTGGTGTCGTGTGTTACCGAGTGTGAGGTGTCGTCGTTCGGGACAGCATTCCGTCGTTCAATTCAACGGATTATGTATGTGCACCTTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.90%	31.70%	0.13%	3.26%	NA
All Indica	2759	95.40%	1.00%	0.22%	3.37%	NA
All Japonica	1512	8.10%	90.70%	0.00%	1.26%	NA
Aus	269	83.30%	1.10%	0.00%	15.61%	NA
Indica I	595	97.10%	1.20%	0.17%	1.51%	NA
Indica II	465	91.80%	0.60%	0.43%	7.10%	NA
Indica III	913	98.60%	0.30%	0.00%	1.10%	NA
Indica Intermediate	786	92.50%	1.90%	0.38%	5.22%	NA
Temperate Japonica	767	3.90%	93.60%	0.00%	2.48%	NA
Tropical Japonica	504	11.10%	88.90%	0.00%	0.00%	NA
Japonica Intermediate	241	14.90%	85.10%	0.00%	0.00%	NA
VI/Aromatic	96	31.20%	68.80%	0.00%	0.00%	NA
Intermediate	90	64.40%	35.60%	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
vg1119375381	A -> DEL	N	N	silent_mutation	Average:37.988; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg1119375381	A -> G	LOC_Os11g32790.1	upstream_gene_variant ; 4769.0bp to feature; MODIFIER	silent_mutation	Average:37.988; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg1119375381	A -> G	LOC_Os11g32800.1	downstream_gene_variant ; 107.0bp to feature; MODIFIER	silent_mutation	Average:37.988; most accessible tissue: Zhenshan97 panicle, score: 86.058	N	N	N	N
vg1119375381	A -> G	LOC_Os11g32790-LOC_Os11g32800	intergenic_region ; MODIFIER	silent_mutation	Average:37.988; most accessible tissue: Zhenshan97 panicle, score: 86.058	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)
vg1119375381	A	G	-0.07	-0.02	-0.01	-0.02	-0.03	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119375381	NA	1.88E-14	mr1376	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
vg1119375381	NA	1.88E-14	mr1431	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
vg1119375381	7.48E-06	7.48E-06	mr1655	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
vg1119375381	NA	3.63E-35	mr1670	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
vg1119375381	NA	1.34E-22	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
vg1119375381	NA	2.09E-06	mr1712	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
vg1119375381	1.51E-07	1.51E-07	mr1770	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
vg1119375381	4.53E-06	NA	mr1829	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
vg1119375381	4.18E-07	NA	mr1829	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
vg1119375381	NA	5.50E-12	mr1940	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
vg1119375381	NA	8.10E-08	mr1354_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
vg1119375381	7.05E-06	NA	mr1829_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
vg1119375381	7.90E-06	NA	mr1842_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