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Detailed information for vg0105145738:

Variant ID: vg0105145738 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 5145738
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTATTATAATATATATACGTAGAGTGGGTAGTAAGATATGACCCATCTAAATTTTTTTTTCAAACATGTGTAATGCCACAATTAAAAAAAAGACGAGATC[T/C]
ATATGAAGTGCTAATACCTAGTAGTAAACTTATACCCTGATAGTAGTTGTTACCACCTCCACAATGTATATTACCTAGTAATAGGGATGCATTCAATGCT

Reverse complement sequence

AGCATTGAATGCATCCCTATTACTAGGTAATATACATTGTGGAGGTGGTAACAACTACTATCAGGGTATAAGTTTACTACTAGGTATTAGCACTTCATAT[A/G]
GATCTCGTCTTTTTTTTAATTGTGGCATTACACATGTTTGAAAAAAAAATTTAGATGGGTCATATCTTACTACCCACTCTACGTATATATATTATAATAC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.60%	7.40%	0.00%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	78.30%	21.70%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	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	85.30%	14.70%	0.00%	0.00%	NA
Tropical Japonica	504	65.90%	34.10%	0.00%	0.00%	NA
Japonica Intermediate	241	82.20%	17.80%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	96.70%	3.30%	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
vg0105145738	T -> C	LOC_Os01g09890.1	upstream_gene_variant ; 4813.0bp to feature; MODIFIER	silent_mutation	Average:66.412; most accessible tissue: Minghui63 root, score: 88.891	N	N	N	N
vg0105145738	T -> C	LOC_Os01g09900.1	upstream_gene_variant ; 2956.0bp to feature; MODIFIER	silent_mutation	Average:66.412; most accessible tissue: Minghui63 root, score: 88.891	N	N	N	N
vg0105145738	T -> C	LOC_Os01g09890-LOC_Os01g09900	intergenic_region ; MODIFIER	silent_mutation	Average:66.412; most accessible tissue: Minghui63 root, score: 88.891	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)
vg0105145738	T	C	-0.01	0.01	0.0	-0.01	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0105145738	1.91E-25	3.40E-27	mr1057	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
vg0105145738	3.02E-15	4.47E-21	mr1057	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
vg0105145738	6.75E-07	NA	mr1238	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
vg0105145738	1.75E-06	NA	mr1309	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
vg0105145738	NA	6.21E-06	mr1309	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
vg0105145738	NA	7.67E-06	mr1677	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
vg0105145738	4.69E-06	NA	mr1841	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
vg0105145738	4.20E-06	NA	mr1900	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
vg0105145738	1.35E-36	4.83E-41	mr1057_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
vg0105145738	3.13E-20	1.14E-25	mr1057_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
vg0105145738	3.97E-07	NA	mr1238_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
vg0105145738	3.07E-06	NA	mr1484_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
vg0105145738	2.29E-07	NA	mr1841_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
vg0105145738	7.63E-06	NA	mr1900_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
vg0105145738	9.34E-06	NA	mr1945_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