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Detailed information for vg0317037478:

Variant ID: vg0317037478 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 17037478
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGGCACCACTTCTTATTTATCTCATGGCTAACCGTCCTCGGATAAGGAGGAGAAGTGGTGCTGGGAGGGAGGAGGGACGACCACGAGAAAAGATAAAAGA[C/T]
ATAGGGAGATGGAGTGGGAGCGAAGGAGGAGCAAGGGAAAGTGCTGGCTTCTCTTAGACCGTTAGACGTCGACCGTTGGGAGAGAACTACGCGTCGGACG

Reverse complement sequence

CGTCCGACGCGTAGTTCTCTCCCAACGGTCGACGTCTAACGGTCTAAGAGAAGCCAGCACTTTCCCTTGCTCCTCCTTCGCTCCCACTCCATCTCCCTAT[G/A]
TCTTTTATCTTTTCTCGTGGTCGTCCCTCCTCCCTCCCAGCACCACTTCTCCTCCTTATCCGAGGACGGTTAGCCATGAGATAAATAAGAAGTGGTGCCG

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	94.80%	3.70%	0.04%	1.48%	NA
All Indica	2759	99.90%	0.00%	0.00%	0.14%	NA
All Japonica	1512	88.40%	11.40%	0.07%	0.13%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	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	99.70%	0.00%	0.00%	0.33%	NA
Indica Intermediate	786	99.90%	0.00%	0.00%	0.13%	NA
Temperate Japonica	767	78.40%	21.50%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	3.30%	0.00%	0.83%	NA
VI/Aromatic	96	36.50%	1.00%	1.04%	61.46%	NA
Intermediate	90	94.40%	1.10%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0317037478	C -> T	LOC_Os03g29900.1	upstream_gene_variant ; 2252.0bp to feature; MODIFIER	silent_mutation	Average:70.371; most accessible tissue: Zhenshan97 flower, score: 88.518	N	N	N	N
vg0317037478	C -> T	LOC_Os03g29910.1	upstream_gene_variant ; 1820.0bp to feature; MODIFIER	silent_mutation	Average:70.371; most accessible tissue: Zhenshan97 flower, score: 88.518	N	N	N	N
vg0317037478	C -> T	LOC_Os03g29910.2	upstream_gene_variant ; 1820.0bp to feature; MODIFIER	silent_mutation	Average:70.371; most accessible tissue: Zhenshan97 flower, score: 88.518	N	N	N	N
vg0317037478	C -> T	LOC_Os03g29900-LOC_Os03g29910	intergenic_region ; MODIFIER	silent_mutation	Average:70.371; most accessible tissue: Zhenshan97 flower, score: 88.518	N	N	N	N
vg0317037478	C -> DEL	N	N	silent_mutation	Average:70.371; most accessible tissue: Zhenshan97 flower, score: 88.518	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)
vg0317037478	C	T	0.03	0.01	0.0	0.01	0.01	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0317037478	1.30E-08	5.11E-12	mr1210	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
vg0317037478	2.44E-07	8.97E-10	mr1305	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
vg0317037478	4.68E-07	4.68E-07	mr1409	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
vg0317037478	1.99E-08	2.44E-12	mr1585	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
vg0317037478	1.00E-08	9.24E-12	mr1586	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
vg0317037478	NA	3.69E-08	mr1765	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
vg0317037478	NA	2.07E-06	mr1793	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
vg0317037478	4.17E-07	3.82E-10	mr1305_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
vg0317037478	3.07E-07	3.07E-07	mr1559_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
vg0317037478	7.40E-08	1.58E-12	mr1585_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
vg0317037478	NA	9.89E-06	mr1765_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
vg0317037478	1.99E-06	4.53E-09	mr1793_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