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Detailed information for vg0714864470:

Variant ID: vg0714864470 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 14864470
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATTATACTGTTTGAAAATTGGGAACAGCGCCAAACGGGCAGACAAAGTTGATTTGGATCCAATAACGAAACATCCCAGCACGAATCTTGGAGCCGGATC[A/G]
AACAGCCAACAAATCGACAGTGTTTAGCGCTGAAAACTGTCGACAGATAAGTAGCAAAACCGTTTGTTTTTCACTCACCTTAACTTTGCATCTGACGGCA

Reverse complement sequence

TGCCGTCAGATGCAAAGTTAAGGTGAGTGAAAAACAAACGGTTTTGCTACTTATCTGTCGACAGTTTTCAGCGCTAAACACTGTCGATTTGTTGGCTGTT[T/C]
GATCCGGCTCCAAGATTCGTGCTGGGATGTTTCGTTATTGGATCCAAATCAACTTTGTCTGCCCGTTTGGCGCTGTTCCCAATTTTCAAACAGTATAATG

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	50.90%	36.60%	1.63%	10.90%	NA
All Indica	2759	81.70%	9.00%	1.27%	8.08%	NA
All Japonica	1512	1.70%	90.30%	2.38%	5.62%	NA
Aus	269	19.30%	10.80%	1.12%	68.77%	NA
Indica I	595	67.10%	16.10%	2.86%	13.95%	NA
Indica II	465	80.40%	12.90%	1.51%	5.16%	NA
Indica III	913	95.30%	0.80%	0.22%	3.72%	NA
Indica Intermediate	786	77.70%	10.70%	1.15%	10.43%	NA
Temperate Japonica	767	2.30%	95.20%	1.04%	1.43%	NA
Tropical Japonica	504	0.40%	86.30%	5.16%	8.13%	NA
Japonica Intermediate	241	2.50%	83.00%	0.83%	13.69%	NA
VI/Aromatic	96	42.70%	45.80%	0.00%	11.46%	NA
Intermediate	90	35.60%	48.90%	3.33%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0714864470	A -> DEL	N	N	silent_mutation	Average:46.175; most accessible tissue: Callus, score: 95.142	N	N	N	N
vg0714864470	A -> G	LOC_Os07g25890.1	upstream_gene_variant ; 1665.0bp to feature; MODIFIER	silent_mutation	Average:46.175; most accessible tissue: Callus, score: 95.142	N	N	N	N
vg0714864470	A -> G	LOC_Os07g25880.1	downstream_gene_variant ; 1114.0bp to feature; MODIFIER	silent_mutation	Average:46.175; most accessible tissue: Callus, score: 95.142	N	N	N	N
vg0714864470	A -> G	LOC_Os07g25900.1	downstream_gene_variant ; 3994.0bp to feature; MODIFIER	silent_mutation	Average:46.175; most accessible tissue: Callus, score: 95.142	N	N	N	N
vg0714864470	A -> G	LOC_Os07g25880-LOC_Os07g25890	intergenic_region ; MODIFIER	silent_mutation	Average:46.175; most accessible tissue: Callus, score: 95.142	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)
vg0714864470	A	G	0.08	0.16	0.12	0.1	0.11	0.11

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0714864470	NA	2.15E-24	mr1537	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
vg0714864470	NA	9.38E-67	mr1538	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
vg0714864470	NA	6.60E-22	mr1541	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
vg0714864470	NA	1.51E-10	mr1630	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
vg0714864470	NA	1.62E-78	mr1718	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
vg0714864470	NA	4.84E-34	mr1737	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
vg0714864470	NA	2.50E-38	mr1890	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
vg0714864470	NA	1.08E-13	mr1326_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