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Detailed information for vg0411899064:

Variant ID: vg0411899064 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 11899064
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATAAAATCTAAAAACAAATCAGTCATAGCCAGCAGACGGGGGTGAGGAGGAGGAGGGCCCCGCCCGGCCGCCGCCGCCGCCTCCTCCACCGGGCTGCCAC[C/T]
CGGCCACCCTCCCATCCTATCGCCTCCCCTCCCGCCGGATCTGGCAGAGGGGAGGCCGCCGCCTCGTGCGCCGTTGCCCGCCTCTCCCGCCGGCTCCTCT

Reverse complement sequence

AGAGGAGCCGGCGGGAGAGGCGGGCAACGGCGCACGAGGCGGCGGCCTCCCCTCTGCCAGATCCGGCGGGAGGGGAGGCGATAGGATGGGAGGGTGGCCG[G/A]
GTGGCAGCCCGGTGGAGGAGGCGGCGGCGGCGGCCGGGCGGGGCCCTCCTCCTCCTCACCCCCGTCTGCTGGCTATGACTGATTTGTTTTTAGATTTTAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.50%	6.20%	0.28%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	85.40%	13.80%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	91.90%	8.00%	0.13%	0.00%	NA
Tropical Japonica	504	82.90%	15.50%	1.59%	0.00%	NA
Japonica Intermediate	241	69.70%	29.00%	1.24%	0.00%	NA
VI/Aromatic	96	22.90%	76.00%	1.04%	0.00%	NA
Intermediate	90	88.90%	11.10%	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
vg0411899064	C -> T	LOC_Os04g21140.1	upstream_gene_variant ; 971.0bp to feature; MODIFIER	silent_mutation	Average:81.734; most accessible tissue: Minghui63 flag leaf, score: 86.911	N	N	N	N
vg0411899064	C -> T	LOC_Os04g21130.1	downstream_gene_variant ; 520.0bp to feature; MODIFIER	silent_mutation	Average:81.734; most accessible tissue: Minghui63 flag leaf, score: 86.911	N	N	N	N
vg0411899064	C -> T	LOC_Os04g21130-LOC_Os04g21140	intergenic_region ; MODIFIER	silent_mutation	Average:81.734; most accessible tissue: Minghui63 flag leaf, score: 86.911	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)
vg0411899064	C	T	-0.02	-0.01	-0.01	-0.02	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0411899064	1.20E-07	3.60E-09	mr1343	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
vg0411899064	2.70E-06	2.70E-06	mr1343	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
vg0411899064	8.03E-08	3.96E-12	mr1829	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
vg0411899064	3.01E-07	NA	mr1842	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
vg0411899064	1.38E-07	5.74E-14	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
vg0411899064	1.63E-06	1.25E-16	mr1842_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
vg0411899064	9.87E-07	5.50E-15	mr1902_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