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Detailed information for vg0434724778:

Variant ID: vg0434724778 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 34724778
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

GCGGCCGGCCGAAGGGGAGAGAAGAGAAAGGGAAAGAAAGAGAGAAGGGAGGAAGAGCGGAGGAAGAAGAAGAGAGAGGATGGCATGTGGGCCCCACATG[G/T]
CAGTGGGTCCCACACTATATATTTTTTGAATGACAAATGGGCCCCACACTTTTTTTTTTATTTCTAGTGCCACTTAAGCGCCACATCAACGCCACATGGA

Reverse complement sequence

TCCATGTGGCGTTGATGTGGCGCTTAAGTGGCACTAGAAATAAAAAAAAAAGTGTGGGGCCCATTTGTCATTCAAAAAATATATAGTGTGGGACCCACTG[C/A]
CATGTGGGGCCCACATGCCATCCTCTCTCTTCTTCTTCCTCCGCTCTTCCTCCCTTCTCTCTTTCTTTCCCTTTCTCTTCTCTCCCCTTCGGCCGGCCGC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.80%	31.80%	0.11%	0.28%	NA
All Indica	2759	97.70%	1.70%	0.18%	0.40%	NA
All Japonica	1512	13.10%	86.80%	0.00%	0.07%	NA
Aus	269	85.50%	14.50%	0.00%	0.00%	NA
Indica I	595	98.00%	1.30%	0.00%	0.67%	NA
Indica II	465	98.10%	0.90%	0.65%	0.43%	NA
Indica III	913	98.60%	1.30%	0.00%	0.11%	NA
Indica Intermediate	786	96.20%	3.10%	0.25%	0.51%	NA
Temperate Japonica	767	4.60%	95.30%	0.00%	0.13%	NA
Tropical Japonica	504	8.10%	91.90%	0.00%	0.00%	NA
Japonica Intermediate	241	50.60%	49.40%	0.00%	0.00%	NA
VI/Aromatic	96	35.40%	64.60%	0.00%	0.00%	NA
Intermediate	90	54.40%	44.40%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0434724778	G -> DEL	N	N	silent_mutation	Average:99.454; most accessible tissue: Zhenshan97 flag leaf, score: 99.924	N	N	N	N
vg0434724778	G -> T	LOC_Os04g58330.1	upstream_gene_variant ; 3528.0bp to feature; MODIFIER	silent_mutation	Average:99.454; most accessible tissue: Zhenshan97 flag leaf, score: 99.924	N	N	N	N
vg0434724778	G -> T	LOC_Os04g58340.1	upstream_gene_variant ; 2.0bp to feature; MODIFIER	silent_mutation	Average:99.454; most accessible tissue: Zhenshan97 flag leaf, score: 99.924	N	N	N	N
vg0434724778	G -> T	LOC_Os04g58350.1	upstream_gene_variant ; 663.0bp to feature; MODIFIER	silent_mutation	Average:99.454; most accessible tissue: Zhenshan97 flag leaf, score: 99.924	N	N	N	N
vg0434724778	G -> T	LOC_Os04g58340-LOC_Os04g58350	intergenic_region ; MODIFIER	silent_mutation	Average:99.454; most accessible tissue: Zhenshan97 flag leaf, score: 99.924	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)
vg0434724778	G	T	-0.03	-0.04	-0.03	-0.02	-0.03	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0434724778	NA	7.79E-23	mr1571	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
vg0434724778	7.90E-07	1.44E-21	mr1580	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
vg0434724778	NA	2.52E-07	mr1604	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
vg0434724778	NA	1.45E-11	mr1683	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
vg0434724778	NA	9.81E-08	mr1693	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
vg0434724778	NA	1.60E-14	mr1924	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
vg0434724778	NA	3.00E-25	mr1350_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
vg0434724778	NA	3.74E-48	mr1519_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
vg0434724778	NA	1.39E-06	mr1691_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
vg0434724778	NA	2.40E-06	mr1720_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
vg0434724778	NA	5.69E-06	mr1745_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