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Detailed information for vg0430538279:

Variant ID: vg0430538279 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30538279
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCACGTACTAAATTTTTTTGGCTGACTAGGATGCCACGTCTGCGAAACCACCCACATATACTGTCATGGGACCTCCTTTGAACAGTTTGCGTGAGTTTAG[G/T]
GGTATACATTTCTGGTTTTGTGGTTAAGGGACCTCAAAAAATCTCGCTGTTAAGTTGAGGGACCTCCGGTGAACTTATTCCTTTATGCAATGTTTGTCTT

Reverse complement sequence

AAGACAAACATTGCATAAAGGAATAAGTTCACCGGAGGTCCCTCAACTTAACAGCGAGATTTTTTGAGGTCCCTTAACCACAAAACCAGAAATGTATACC[C/A]
CTAAACTCACGCAAACTGTTCAAAGGAGGTCCCATGACAGTATATGTGGGTGGTTTCGCAGACGTGGCATCCTAGTCAGCCAAAAAAATTTAGTACGTGG

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	75.10%	24.80%	0.04%	0.00%	NA
All Indica	2759	76.90%	23.00%	0.07%	0.00%	NA
All Japonica	1512	79.80%	20.20%	0.00%	0.00%	NA
Aus	269	19.00%	81.00%	0.00%	0.00%	NA
Indica I	595	56.30%	43.40%	0.34%	0.00%	NA
Indica II	465	93.10%	6.90%	0.00%	0.00%	NA
Indica III	913	78.50%	21.50%	0.00%	0.00%	NA
Indica Intermediate	786	81.20%	18.80%	0.00%	0.00%	NA
Temperate Japonica	767	94.90%	5.10%	0.00%	0.00%	NA
Tropical Japonica	504	69.60%	30.40%	0.00%	0.00%	NA
Japonica Intermediate	241	52.70%	47.30%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	84.40%	15.60%	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
vg0430538279	G -> T	LOC_Os04g51540.1	upstream_gene_variant ; 1970.0bp to feature; MODIFIER	silent_mutation	Average:97.677; most accessible tissue: Minghui63 panicle, score: 99.231	N	N	N	N
vg0430538279	G -> T	LOC_Os04g51550.1	downstream_gene_variant ; 426.0bp to feature; MODIFIER	silent_mutation	Average:97.677; most accessible tissue: Minghui63 panicle, score: 99.231	N	N	N	N
vg0430538279	G -> T	LOC_Os04g51550-LOC_Os04g51560	intergenic_region ; MODIFIER	silent_mutation	Average:97.677; most accessible tissue: Minghui63 panicle, score: 99.231	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)
vg0430538279	G	T	0.01	0.01	0.01	0.01	0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430538279	NA	1.24E-08	mr1064	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
vg0430538279	NA	1.54E-09	mr1534	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
vg0430538279	1.44E-09	NA	mr1745	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
vg0430538279	4.57E-09	2.94E-14	mr1745	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
vg0430538279	NA	6.88E-07	mr1042_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
vg0430538279	2.23E-07	2.88E-12	mr1064_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
vg0430538279	1.28E-11	NA	mr1745_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
vg0430538279	4.76E-13	9.29E-24	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