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Detailed information for vg1125651425:

Variant ID: vg1125651425 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25651425
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCATCATTGTTGTCTCTGTAAGCAACTGGTGAGCATGTGTAACTAAAATTTTGATATGAGTACAAGTTTAGAGCATTTGAGATATTGTAGAGCTCAAGC[G/A]
AATTTTTGTCAAGTCTCCTGAGATGTGTAACACATCTGGTCGCCGCCTTCGTGTGGTTTGACGGGCATGTCTTAGGCTGAAGTTGACTGGCACGCTGAGT

Reverse complement sequence

ACTCAGCGTGCCAGTCAACTTCAGCCTAAGACATGCCCGTCAAACCACACGAAGGCGGCGACCAGATGTGTTACACATCTCAGGAGACTTGACAAAAATT[C/T]
GCTTGAGCTCTACAATATCTCAAATGCTCTAAACTTGTACTCATATCAAAATTTTAGTTACACATGCTCACCAGTTGCTTACAGAGACAACAATGATGAT

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	86.00%	2.90%	7.45%	3.64%	NA
All Indica	2759	87.50%	2.80%	6.96%	2.79%	NA
All Japonica	1512	83.90%	2.20%	8.47%	5.36%	NA
Aus	269	84.80%	6.30%	7.43%	1.49%	NA
Indica I	595	94.30%	0.20%	4.20%	1.34%	NA
Indica II	465	73.10%	7.50%	14.84%	4.52%	NA
Indica III	913	93.60%	0.70%	3.83%	1.86%	NA
Indica Intermediate	786	83.60%	4.50%	8.02%	3.94%	NA
Temperate Japonica	767	79.70%	4.00%	10.56%	5.74%	NA
Tropical Japonica	504	88.50%	0.00%	6.94%	4.56%	NA
Japonica Intermediate	241	88.00%	1.20%	4.98%	5.81%	NA
VI/Aromatic	96	82.30%	8.30%	5.21%	4.17%	NA
Intermediate	90	82.20%	3.30%	7.78%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125651425	G -> A	LOC_Os11g42610.1	downstream_gene_variant ; 337.0bp to feature; MODIFIER	silent_mutation	Average:52.833; most accessible tissue: Minghui63 young leaf, score: 87.677	N	N	N	N
vg1125651425	G -> A	LOC_Os11g42610-LOC_Os11g42620	intergenic_region ; MODIFIER	silent_mutation	Average:52.833; most accessible tissue: Minghui63 young leaf, score: 87.677	N	N	N	N
vg1125651425	G -> DEL	N	N	silent_mutation	Average:52.833; most accessible tissue: Minghui63 young leaf, score: 87.677	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)
vg1125651425	G	A	-0.07	-0.03	-0.02	-0.03	-0.05	-0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125651425	NA	9.34E-06	mr1122	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
vg1125651425	NA	7.90E-06	mr1310	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
vg1125651425	4.88E-07	4.88E-07	mr1663	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
vg1125651425	NA	6.89E-10	mr1889	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
vg1125651425	NA	1.42E-11	mr1907	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
vg1125651425	NA	1.75E-09	mr1934	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
vg1125651425	NA	2.91E-06	mr1310_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