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Detailed information for vg0419832144:

Variant ID: vg0419832144 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 19832144
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTTTGGGGTACTACTCAGGTCACTATAACCACTAGGCTACATGCCCTTTCGTACAAAATTTAAAAATTTAAAAGAGAAAAATAAACTAGAAGTAAGATAA[G/A]
CCGGTAAAAAACCCACTTGTCCGTCCCGCTTGCATCCCTAGAAAATTTCAGCACGATCGATCGAATCGTGCTAAAAAGTTTCAGCACGGAGAGCTCGCGA

Reverse complement sequence

TCGCGAGCTCTCCGTGCTGAAACTTTTTAGCACGATTCGATCGATCGTGCTGAAATTTTCTAGGGATGCAAGCGGGACGGACAAGTGGGTTTTTTACCGG[C/T]
TTATCTTACTTCTAGTTTATTTTTCTCTTTTAAATTTTTAAATTTTGTACGAAAGGGCATGTAGCCTAGTGGTTATAGTGACCTGAGTAGTACCCCAAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.60%	7.10%	1.06%	16.23%	NA
All Indica	2759	71.40%	1.00%	0.18%	27.47%	NA
All Japonica	1512	77.80%	19.20%	2.71%	0.20%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	93.40%	0.00%	0.17%	6.39%	NA
Indica II	465	66.90%	2.80%	0.22%	30.11%	NA
Indica III	913	61.40%	0.10%	0.11%	38.34%	NA
Indica Intermediate	786	68.80%	1.70%	0.25%	29.26%	NA
Temperate Japonica	767	95.40%	2.10%	2.48%	0.00%	NA
Tropical Japonica	504	51.60%	45.60%	2.18%	0.60%	NA
Japonica Intermediate	241	76.80%	18.70%	4.56%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	74.40%	17.80%	3.33%	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
vg0419832144	G -> DEL	N	N	silent_mutation	Average:76.763; most accessible tissue: Minghui63 young leaf, score: 97.49	N	N	N	N
vg0419832144	G -> A	LOC_Os04g32840.1	upstream_gene_variant ; 4242.0bp to feature; MODIFIER	silent_mutation	Average:76.763; most accessible tissue: Minghui63 young leaf, score: 97.49	N	N	N	N
vg0419832144	G -> A	LOC_Os04g32850.1	downstream_gene_variant ; 2987.0bp to feature; MODIFIER	silent_mutation	Average:76.763; most accessible tissue: Minghui63 young leaf, score: 97.49	N	N	N	N
vg0419832144	G -> A	LOC_Os04g32850.3	downstream_gene_variant ; 2987.0bp to feature; MODIFIER	silent_mutation	Average:76.763; most accessible tissue: Minghui63 young leaf, score: 97.49	N	N	N	N
vg0419832144	G -> A	LOC_Os04g32850.2	downstream_gene_variant ; 2987.0bp to feature; MODIFIER	silent_mutation	Average:76.763; most accessible tissue: Minghui63 young leaf, score: 97.49	N	N	N	N
vg0419832144	G -> A	LOC_Os04g32840-LOC_Os04g32850	intergenic_region ; MODIFIER	silent_mutation	Average:76.763; most accessible tissue: Minghui63 young leaf, score: 97.49	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)
vg0419832144	G	A	-0.04	0.01	-0.01	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0419832144	3.54E-06	NA	mr1226	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
vg0419832144	NA	3.21E-14	mr1410	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
vg0419832144	6.93E-06	NA	mr1070_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
vg0419832144	5.59E-09	NA	mr1083_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
vg0419832144	2.22E-07	NA	mr1085_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
vg0419832144	3.28E-07	NA	mr1103_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
vg0419832144	7.82E-11	NA	mr1104_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
vg0419832144	3.31E-08	NA	mr1107_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
vg0419832144	4.31E-07	NA	mr1145_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
vg0419832144	NA	9.44E-06	mr1155_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
vg0419832144	1.18E-08	NA	mr1226_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
vg0419832144	7.02E-06	NA	mr1264_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
vg0419832144	2.97E-06	NA	mr1408_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
vg0419832144	NA	3.14E-06	mr1574_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