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Detailed information for vg0230660705:

Variant ID: vg0230660705 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 30660705
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTTTGAAGCGAAATGGATGGTAATTCCCATACTTAATCTGGTATAATTCTAGAATTTTCTTCATCGTAACATAAAATTTGGTTTCTAATTGGTACTTCCT[C/T]
TGTTTCATAATGTAAATCATTCTAACATTTCTCCATTCATATTGATGTTAATGAATCTAAATATATATATCTATCTATATTCATTAACATCAATATAAAT

Reverse complement sequence

ATTTATATTGATGTTAATGAATATAGATAGATATATATATTTAGATTCATTAACATCAATATGAATGGAGAAATGTTAGAATGATTTACATTATGAAACA[G/A]
AGGAAGTACCAATTAGAAACCAAATTTTATGTTACGATGAAGAAAATTCTAGAATTATACCAGATTAAGTATGGGAATTACCATCCATTTCGCTTCAAAC

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	70.20%	7.70%	13.99%	8.10%	NA
All Indica	2759	56.10%	7.60%	22.87%	13.37%	NA
All Japonica	1512	99.70%	0.20%	0.07%	0.07%	NA
Aus	269	33.10%	55.00%	8.18%	3.72%	NA
Indica I	595	44.40%	3.20%	38.82%	13.61%	NA
Indica II	465	59.10%	10.30%	17.85%	12.69%	NA
Indica III	913	63.60%	5.90%	14.35%	16.10%	NA
Indica Intermediate	786	54.60%	11.30%	23.66%	10.43%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	84.40%	5.60%	6.67%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0230660705	C -> T	LOC_Os02g50220.1	upstream_gene_variant ; 611.0bp to feature; MODIFIER	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 94.522	N	N	N	N
vg0230660705	C -> T	LOC_Os02g50200.1	downstream_gene_variant ; 4253.0bp to feature; MODIFIER	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 94.522	N	N	N	N
vg0230660705	C -> T	LOC_Os02g50210.1	downstream_gene_variant ; 1354.0bp to feature; MODIFIER	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 94.522	N	N	N	N
vg0230660705	C -> T	LOC_Os02g50210-LOC_Os02g50220	intergenic_region ; MODIFIER	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 94.522	N	N	N	N
vg0230660705	C -> DEL	N	N	silent_mutation	Average:66.953; most accessible tissue: Callus, score: 94.522	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)
vg0230660705	C	T	-0.01	-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
vg0230660705	NA	2.92E-06	mr1082	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
vg0230660705	NA	5.06E-06	mr1241	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
vg0230660705	NA	9.81E-07	mr1437	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
vg0230660705	NA	3.78E-09	mr1070_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
vg0230660705	NA	5.53E-08	mr1088_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
vg0230660705	NA	2.43E-10	mr1241_2	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
vg0230660705	NA	2.59E-07	mr1264_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
vg0230660705	NA	5.21E-09	mr1437_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
vg0230660705	NA	2.01E-08	mr1949_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