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Detailed information for vg1203760773:

Variant ID: vg1203760773 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 3760773
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCGCTAATTAAATCGGCATTGAACCGGTATCGATCATTGCATGAGCAAGAGCGCTCCGCTGCCGCGCGGTCTCGCGCGATACTGCCCGCGACGTCATTT[C/T]
CACGTCACTTTTGCGCAACGGTTGTACGAGACCGATGGTATATTTTTGTAAAAAATTTTGCATCCCGAATATTCCTGAGAAAAAAAATTGAATGAATAGT

Reverse complement sequence

ACTATTCATTCAATTTTTTTTCTCAGGAATATTCGGGATGCAAAATTTTTTACAAAAATATACCATCGGTCTCGTACAACCGTTGCGCAAAAGTGACGTG[G/A]
AAATGACGTCGCGGGCAGTATCGCGCGAGACCGCGCGGCAGCGGAGCGCTCTTGCTCATGCAATGATCGATACCGGTTCAATGCCGATTTAATTAGCGAT

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	72.20%	27.50%	0.34%	0.00%	NA
All Indica	2759	98.40%	1.50%	0.11%	0.00%	NA
All Japonica	1512	24.70%	74.50%	0.79%	0.00%	NA
Aus	269	92.60%	7.10%	0.37%	0.00%	NA
Indica I	595	99.70%	0.30%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	98.10%	1.80%	0.11%	0.00%	NA
Indica Intermediate	786	97.50%	2.30%	0.25%	0.00%	NA
Temperate Japonica	767	33.80%	65.20%	1.04%	0.00%	NA
Tropical Japonica	504	10.70%	88.70%	0.60%	0.00%	NA
Japonica Intermediate	241	25.30%	74.30%	0.41%	0.00%	NA
VI/Aromatic	96	22.90%	77.10%	0.00%	0.00%	NA
Intermediate	90	55.60%	44.40%	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
vg1203760773	C -> T	LOC_Os12g07540.1	downstream_gene_variant ; 2222.0bp to feature; MODIFIER	silent_mutation	Average:81.75; most accessible tissue: Minghui63 young leaf, score: 94.027	N	N	N	N
vg1203760773	C -> T	LOC_Os12g07550.1	downstream_gene_variant ; 937.0bp to feature; MODIFIER	silent_mutation	Average:81.75; most accessible tissue: Minghui63 young leaf, score: 94.027	N	N	N	N
vg1203760773	C -> T	LOC_Os12g07540-LOC_Os12g07550	intergenic_region ; MODIFIER	silent_mutation	Average:81.75; most accessible tissue: Minghui63 young leaf, score: 94.027	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)
vg1203760773	C	T	0.1	0.14	0.11	0.0	0.04	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1203760773	NA	2.31E-07	mr1002	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
vg1203760773	NA	2.85E-11	mr1070	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
vg1203760773	NA	6.41E-11	mr1128	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
vg1203760773	4.19E-07	NA	mr1002_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
vg1203760773	NA	5.02E-11	mr1002_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
vg1203760773	NA	8.59E-15	mr1148_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
vg1203760773	NA	9.81E-09	mr1222_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
vg1203760773	NA	5.62E-07	mr1548_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