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Detailed information for vg0417258890:

Variant ID: vg0417258890 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 17258890
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGACCAGTTATAATCCGTGTCCAACCTATTGTTTTTTTAGGAAAATCATTCGTGCAATAGTGAATGCTTCCCTGTACTAGTTGCATTAACCCTGACATT[G/A]
CCATGACGATCGCGAAGGTAGCCATCGGCAGCGTCTCGCAACAACGAGCAGACCCTCGCCTCGGTGAACACCTTCCCCGGCCGGCAGAAGTAGCCCAGCT

Reverse complement sequence

AGCTGGGCTACTTCTGCCGGCCGGGGAAGGTGTTCACCGAGGCGAGGGTCTGCTCGTTGTTGCGAGACGCTGCCGATGGCTACCTTCGCGATCGTCATGG[C/T]
AATGTCAGGGTTAATGCAACTAGTACAGGGAAGCATTCACTATTGCACGAATGATTTTCCTAAAAAAACAATAGGTTGGACACGGATTATAACTGGTCGT

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	91.40%	6.30%	2.37%	0.00%	NA
All Indica	2759	96.20%	1.80%	1.99%	0.00%	NA
All Japonica	1512	80.70%	15.70%	3.57%	0.00%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	88.60%	4.90%	6.55%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	96.30%	2.00%	1.65%	0.00%	NA
Temperate Japonica	767	93.50%	1.80%	4.69%	0.00%	NA
Tropical Japonica	504	62.50%	34.70%	2.78%	0.00%	NA
Japonica Intermediate	241	78.00%	20.30%	1.66%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	5.60%	2.22%	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
vg0417258890	G -> A	LOC_Os04g29090.1	synonymous_variant ; p.Gly645Gly; LOW	synonymous_codon	Average:69.487; most accessible tissue: Minghui63 young leaf, score: 89.871	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)
vg0417258890	G	A	0.07	0.06	0.08	0.03	0.06	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0417258890	4.93E-06	4.93E-06	mr1245_2	Jap_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
vg0417258890	NA	2.14E-06	mr1363_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
vg0417258890	9.06E-06	9.05E-06	mr1373_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
vg0417258890	NA	3.88E-06	mr1397_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
vg0417258890	3.25E-06	3.24E-06	mr1663_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
vg0417258890	4.41E-06	4.41E-06	mr1669_2	Jap_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
vg0417258890	7.36E-06	7.36E-06	mr1688_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
vg0417258890	5.50E-06	5.50E-06	mr1822_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
vg0417258890	NA	6.41E-06	mr1833_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