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Detailed information for vg0141963794:

Variant ID: vg0141963794 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 41963794
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAAATACAAGACCCATTTCACGTTTGCATAGCGCTACAGTATTTTTGGTCTTCTCCAACAATAAGACTTAAAAAATAACCCTTAATGTAAATAGGTCTT[C/T]
AGGAGAGAGAATACTCGGATTTAGATTATGCCTCTTATAGCACGCAAAATGGGTCTTCTGTATAGGTACTCTATTGGAGGCTGAAATAGTACTATCGGAG

Reverse complement sequence

CTCCGATAGTACTATTTCAGCCTCCAATAGAGTACCTATACAGAAGACCCATTTTGCGTGCTATAAGAGGCATAATCTAAATCCGAGTATTCTCTCTCCT[G/A]
AAGACCTATTTACATTAAGGGTTATTTTTTAAGTCTTATTGTTGGAGAAGACCAAAAATACTGTAGCGCTATGCAAACGTGAAATGGGTCTTGTATTTTA

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	70.40%	5.30%	6.88%	17.48%	NA
All Indica	2759	80.40%	0.10%	1.30%	18.16%	NA
All Japonica	1512	49.90%	15.70%	13.76%	20.63%	NA
Aus	269	72.50%	0.00%	27.51%	0.00%	NA
Indica I	595	81.20%	0.00%	1.01%	17.82%	NA
Indica II	465	74.40%	0.00%	2.37%	23.23%	NA
Indica III	913	85.90%	0.10%	0.22%	13.80%	NA
Indica Intermediate	786	77.10%	0.30%	2.16%	20.48%	NA
Temperate Japonica	767	80.40%	5.20%	8.21%	6.13%	NA
Tropical Japonica	504	13.50%	27.60%	19.25%	39.68%	NA
Japonica Intermediate	241	29.00%	24.10%	19.92%	26.97%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	67.80%	10.00%	7.78%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0141963794	C -> T	LOC_Os01g72350.1	upstream_gene_variant ; 332.0bp to feature; MODIFIER	silent_mutation	Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979	N	N	N	N
vg0141963794	C -> T	LOC_Os01g72350.2	upstream_gene_variant ; 332.0bp to feature; MODIFIER	silent_mutation	Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979	N	N	N	N
vg0141963794	C -> T	LOC_Os01g72340.1	downstream_gene_variant ; 1007.0bp to feature; MODIFIER	silent_mutation	Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979	N	N	N	N
vg0141963794	C -> T	LOC_Os01g72340-LOC_Os01g72350	intergenic_region ; MODIFIER	silent_mutation	Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979	N	N	N	N
vg0141963794	C -> DEL	N	N	silent_mutation	Average:88.374; most accessible tissue: Minghui63 young leaf, score: 96.979	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)
vg0141963794	C	T	-0.04	-0.03	-0.01	-0.01	-0.04	-0.08

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0141963794	NA	1.20E-12	mr1449	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
vg0141963794	NA	2.60E-07	mr1668	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
vg0141963794	6.36E-06	1.06E-16	mr1871	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
vg0141963794	1.19E-07	1.92E-26	mr1042_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
vg0141963794	NA	3.57E-08	mr1042_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
vg0141963794	NA	3.80E-09	mr1502_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
vg0141963794	NA	1.31E-08	mr1543_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
vg0141963794	NA	3.62E-12	mr1680_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
vg0141963794	2.85E-06	1.09E-15	mr1742_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
vg0141963794	NA	6.71E-09	mr1742_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
vg0141963794	1.80E-11	2.81E-32	mr1871_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
vg0141963794	NA	4.03E-11	mr1871_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