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Detailed information for vg0723127888:

Variant ID: vg0723127888 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 23127888
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CGTGTCTCCGCGCGGTGACTTCGGGTGCGTGGTGCTTCATATTCTCGACTCCGAGCCCCGAGTCTGGACGTCTCATCTTTTCGTATCTTTGACTTGCTCA[A/G]
TTCGTCTCGAGTCTGGACGTCTCATCTTCTCCGAGCACCAGGCCGCTAGCCGGCTCATCCAATTTCATATTTTCATTCAACCGGCAAATAGCAACTTAGC

Reverse complement sequence

GCTAAGTTGCTATTTGCCGGTTGAATGAAAATATGAAATTGGATGAGCCGGCTAGCGGCCTGGTGCTCGGAGAAGATGAGACGTCCAGACTCGAGACGAA[T/C]
TGAGCAAGTCAAAGATACGAAAAGATGAGACGTCCAGACTCGGGGCTCGGAGTCGAGAATATGAAGCACCACGCACCCGAAGTCACCGCGCGGAGACACG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.10%	8.80%	0.04%	0.00%	NA
All Indica	2759	85.20%	14.70%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	97.50%	2.50%	0.00%	0.00%	NA
Indica II	465	81.70%	17.80%	0.43%	0.00%	NA
Indica III	913	79.50%	20.50%	0.00%	0.00%	NA
Indica Intermediate	786	84.70%	15.30%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0723127888	A -> G	LOC_Os07g38490-LOC_Os07g38500	intergenic_region ; MODIFIER	silent_mutation	Average:79.68; most accessible tissue: Minghui63 panicle, score: 95.966	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)
vg0723127888	A	G	-0.02	-0.03	-0.02	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0723127888	NA	3.27E-06	mr1170	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
vg0723127888	3.01E-06	1.09E-08	mr1304	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
vg0723127888	NA	5.21E-07	mr1376	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
vg0723127888	NA	5.21E-07	mr1431	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
vg0723127888	NA	6.73E-06	mr1743	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
vg0723127888	NA	1.45E-06	mr1820	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
vg0723127888	NA	1.42E-07	mr1830	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
vg0723127888	NA	7.28E-08	mr1951	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
vg0723127888	NA	9.89E-06	mr1958	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