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Detailed information for vg1123564224:

Variant ID: vg1123564224 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23564224
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CCGAGTTCGTTAGTACAGGGTACAGATTTCCAACCGGGTACGCGTGGAAAACGGAACGGTCTATTAGCACGTGATTAATTAAGTATTAGCTAATTTTTTT[A/T]
AAAAAAATGGATTGATTTGATTTTTTAAGCAACTTTCGTATAGAAACTTTTTTGCAAAAAAACACACTGTTTAGCAGTTTAAAAAGCATACGCGCGGAAA

Reverse complement sequence

TTTCCGCGCGTATGCTTTTTAAACTGCTAAACAGTGTGTTTTTTTGCAAAAAAGTTTCTATACGAAAGTTGCTTAAAAAATCAAATCAATCCATTTTTTT[T/A]
AAAAAAATTAGCTAATACTTAATTAATCACGTGCTAATAGACCGTTCCGTTTTCCACGCGTACCCGGTTGGAAATCTGTACCCTGTACTAACGAACTCGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.50%	16.70%	6.09%	6.67%	NA
All Indica	2759	80.80%	2.80%	6.13%	10.26%	NA
All Japonica	1512	48.00%	45.50%	4.43%	2.05%	NA
Aus	269	84.40%	0.40%	15.24%	0.00%	NA
Indica I	595	58.20%	4.70%	2.18%	34.96%	NA
Indica II	465	97.00%	0.40%	1.72%	0.86%	NA
Indica III	913	80.90%	2.80%	13.36%	2.85%	NA
Indica Intermediate	786	88.20%	2.80%	3.31%	5.73%	NA
Temperate Japonica	767	59.60%	29.20%	7.17%	4.04%	NA
Tropical Japonica	504	30.00%	69.60%	0.40%	0.00%	NA
Japonica Intermediate	241	49.00%	46.90%	4.15%	0.00%	NA
VI/Aromatic	96	89.60%	6.20%	4.17%	0.00%	NA
Intermediate	90	73.30%	17.80%	7.78%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1123564224	A -> T	LOC_Os11g39550.1	downstream_gene_variant ; 1012.0bp to feature; MODIFIER	silent_mutation	Average:52.587; most accessible tissue: Callus, score: 95.255	N	N	N	N
vg1123564224	A -> T	LOC_Os11g39540-LOC_Os11g39550	intergenic_region ; MODIFIER	silent_mutation	Average:52.587; most accessible tissue: Callus, score: 95.255	N	N	N	N
vg1123564224	A -> DEL	N	N	silent_mutation	Average:52.587; most accessible tissue: Callus, score: 95.255	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)
vg1123564224	A	T	0.0	0.02	0.02	0.01	0.01	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123564224	NA	3.62E-08	mr1084_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
vg1123564224	NA	2.14E-07	mr1205_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
vg1123564224	NA	8.79E-07	mr1405_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
vg1123564224	NA	8.93E-08	mr1574_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
vg1123564224	6.19E-06	NA	mr1679_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
vg1123564224	4.59E-07	NA	mr1720_2	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
vg1123564224	3.14E-06	NA	mr1829_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