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Detailed information for vg1105893410:

Variant ID: vg1105893410 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5893410
Reference Allele: C	Alternative Allele: T
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:

GAATCTAGGGACACTCCCCATAGGAACTCCAACACGATGAGTTGCTGCCAGGACATTATGAGCAACCGAATGAGTGGAAGTAATTTCTAGGGTGCTAAGA[C/T]
GCGTCTCCTCAGCAATCAGATCTGCAAGAGCCTCTGTCATAGTTGGAAGTGTACTACGCGCAAGCAATTGAACCCGTTTAGGTTCAAATTTAGGGAGAAG

Reverse complement sequence

CTTCTCCCTAAATTTGAACCTAAACGGGTTCAATTGCTTGCGCGTAGTACACTTCCAACTATGACAGAGGCTCTTGCAGATCTGATTGCTGAGGAGACGC[G/A]
TCTTAGCACCCTAGAAATTACTTCCACTCATTCGGTTGCTCATAATGTCCTGGCAGCAACTCATCGTGTTGGAGTTCCTATGGGGAGTGTCCCTAGATTC

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	90.30%	9.70%	0.04%	0.00%	NA
All Indica	2759	84.70%	15.30%	0.04%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	93.30%	6.70%	0.00%	0.00%	NA
Indica I	595	77.00%	22.90%	0.17%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	78.40%	21.60%	0.00%	0.00%	NA
Indica Intermediate	786	89.80%	10.20%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	98.80%	1.20%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	86.70%	12.20%	1.11%	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
vg1105893410	C -> T	LOC_Os11g10740.1	upstream_gene_variant ; 1954.0bp to feature; MODIFIER	silent_mutation	Average:60.16; most accessible tissue: Minghui63 panicle, score: 89.949	N	N	N	N
vg1105893410	C -> T	LOC_Os11g10720.1	downstream_gene_variant ; 1566.0bp to feature; MODIFIER	silent_mutation	Average:60.16; most accessible tissue: Minghui63 panicle, score: 89.949	N	N	N	N
vg1105893410	C -> T	LOC_Os11g10730.1	downstream_gene_variant ; 420.0bp to feature; MODIFIER	silent_mutation	Average:60.16; most accessible tissue: Minghui63 panicle, score: 89.949	N	N	N	N
vg1105893410	C -> T	LOC_Os11g10720-LOC_Os11g10730	intergenic_region ; MODIFIER	silent_mutation	Average:60.16; most accessible tissue: Minghui63 panicle, score: 89.949	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)
vg1105893410	C	T	-0.02	-0.03	-0.03	-0.03	-0.06	-0.07

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105893410	NA	8.64E-08	mr1042	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
vg1105893410	NA	3.71E-08	mr1042	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
vg1105893410	6.62E-06	1.82E-08	mr1043	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
vg1105893410	NA	1.15E-08	mr1043	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
vg1105893410	NA	3.72E-06	mr1180	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
vg1105893410	NA	4.39E-06	mr1282	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
vg1105893410	NA	4.22E-07	mr1912	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
vg1105893410	NA	3.66E-07	mr1912	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
vg1105893410	NA	4.12E-06	mr1043_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
vg1105893410	6.54E-06	3.15E-07	mr1043_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
vg1105893410	NA	9.53E-07	mr1180_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
vg1105893410	NA	5.56E-07	mr1330_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
vg1105893410	NA	3.53E-07	mr1378_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