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Detailed information for vg1004248992:

Variant ID: vg1004248992 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 4248992
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGAACGACTAGAAGCCATCGATCACACTATGATCCATCTTGTGCAGCAGTATACGCCAGACAACCAAATATTTGCGTCTTTTCAAAATTTGACAATTTTC[G/T]
CAAGTCTTTTACTTCTCCACATAGAAAGCTTTCGTTTTTGGTCATTGCTCTCACGGAAATAGCCGTCATGACGTGAGCATAGTAGAAAAAATCGAACCGG

Reverse complement sequence

CCGGTTCGATTTTTTCTACTATGCTCACGTCATGACGGCTATTTCCGTGAGAGCAATGACCAAAAACGAAAGCTTTCTATGTGGAGAAGTAAAAGACTTG[C/A]
GAAAATTGTCAAATTTTGAAAAGACGCAAATATTTGGTTGTCTGGCGTATACTGCTGCACAAGATGGATCATAGTGTGATCGATGGCTTCTAGTCGTTCG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.20%	5.10%	0.17%	0.55%	NA
All Indica	2759	99.40%	0.30%	0.04%	0.25%	NA
All Japonica	1512	86.60%	13.20%	0.13%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.50%	0.10%	0.00%	0.44%	NA
Indica Intermediate	786	98.50%	1.00%	0.13%	0.38%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	66.90%	33.10%	0.00%	0.00%	NA
Japonica Intermediate	241	85.90%	13.30%	0.83%	0.00%	NA
VI/Aromatic	96	53.10%	24.00%	5.21%	17.71%	NA
Intermediate	90	86.70%	11.10%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1004248992	G -> T	LOC_Os10g07970.1	upstream_gene_variant ; 2350.0bp to feature; MODIFIER	silent_mutation	Average:70.218; most accessible tissue: Callus, score: 94.544	N	N	N	N
vg1004248992	G -> T	LOC_Os10g07966.1	downstream_gene_variant ; 3385.0bp to feature; MODIFIER	silent_mutation	Average:70.218; most accessible tissue: Callus, score: 94.544	N	N	N	N
vg1004248992	G -> T	LOC_Os10g07966-LOC_Os10g07970	intergenic_region ; MODIFIER	silent_mutation	Average:70.218; most accessible tissue: Callus, score: 94.544	N	N	N	N
vg1004248992	G -> DEL	N	N	silent_mutation	Average:70.218; most accessible tissue: Callus, score: 94.544	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)
vg1004248992	G	T	0.09	0.09	0.07	0.08	0.06	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1004248992	NA	4.36E-06	mr1068_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
vg1004248992	NA	5.13E-06	mr1077_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
vg1004248992	NA	7.97E-07	mr1096_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
vg1004248992	NA	5.39E-06	mr1112_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
vg1004248992	8.56E-06	6.48E-09	mr1121_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
vg1004248992	NA	5.86E-06	mr1200_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
vg1004248992	NA	5.41E-06	mr1211_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
vg1004248992	NA	2.50E-06	mr1220_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
vg1004248992	NA	6.81E-08	mr1243_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
vg1004248992	NA	3.95E-07	mr1248_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
vg1004248992	NA	7.12E-07	mr1250_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
vg1004248992	1.56E-06	1.56E-06	mr1603_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