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Detailed information for vg0115284393:

Variant ID: vg0115284393 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15284393
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCGTGGAGGAGTTCGGGGCCACGGCGCCGCCCAACTCCGACGAACTGGAGCTCGCGAGGGCGAGGTGGCTGAAGCTGCACGACTGTAAGTGCAGCTCCCG[G/A]
CACTGCGCCCACGAGAACTCCAGCTCGTCGGAGACGGGCGGTGCCGCGGCCTTGAACTCCTCCACGAGCCCATGCGCAGGGTCTGCGTCAGTGCCCGGAT

Reverse complement sequence

ATCCGGGCACTGACGCAGACCCTGCGCATGGGCTCGTGGAGGAGTTCAAGGCCGCGGCACCGCCCGTCTCCGACGAGCTGGAGTTCTCGTGGGCGCAGTG[C/T]
CGGGAGCTGCACTTACAGTCGTGCAGCTTCAGCCACCTCGCCCTCGCGAGCTCCAGTTCGTCGGAGTTGGGCGGCGCCGTGGCCCCGAACTCCTCCACGA

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	70.80%	16.40%	1.57%	11.26%	NA
All Indica	2759	57.50%	25.30%	1.99%	15.22%	NA
All Japonica	1512	90.10%	2.30%	0.73%	6.88%	NA
Aus	269	83.60%	14.10%	1.86%	0.37%	NA
Indica I	595	31.80%	40.20%	2.02%	26.05%	NA
Indica II	465	75.70%	4.10%	2.80%	17.42%	NA
Indica III	913	65.00%	29.20%	0.77%	5.04%	NA
Indica Intermediate	786	57.60%	21.90%	2.93%	17.56%	NA
Temperate Japonica	767	95.20%	0.90%	0.26%	3.65%	NA
Tropical Japonica	504	91.10%	5.00%	0.60%	3.37%	NA
Japonica Intermediate	241	71.80%	1.20%	2.49%	24.48%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	4.40%	3.33%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0115284393	G -> A	LOC_Os01g27370.1	synonymous_variant ; p.Cys106Cys; LOW	synonymous_codon	Average:88.432; most accessible tissue: Minghui63 panicle, score: 97.671	N	N	N	N
vg0115284393	G -> DEL	LOC_Os01g27370.1	N	frameshift_variant	Average:88.432; most accessible tissue: Minghui63 panicle, score: 97.671	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)
vg0115284393	G	A	-0.22	-0.16	-0.15	-0.12	-0.18	-0.18

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115284393	NA	1.80E-06	mr1518	Ind_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
vg0115284393	2.59E-07	NA	mr1519	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
vg0115284393	5.34E-06	3.67E-08	mr1519	Ind_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
vg0115284393	NA	1.40E-07	mr1676	Ind_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
vg0115284393	NA	9.29E-07	mr1105_2	Ind_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
vg0115284393	NA	3.90E-07	mr1232_2	Ind_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
vg0115284393	2.19E-11	NA	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
vg0115284393	4.45E-10	3.94E-18	mr1519_2	Ind_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
vg0115284393	NA	1.28E-07	mr1557_2	Ind_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