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Detailed information for vg1209676708:

Variant ID: vg1209676708 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 9676708
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TACTGTTATGAGACATTAACCGTGCCAACCACAAGCCAGCGTGGGCAACGACTTTACCTTTTGTATAGCATAGTTCATTATGGGGTGCCAGACTGAGAAG[T/C]
GGCGAGAAATCCGTGGGGGTCGCTGGGGAGTCCATGCCTCGGTGATTATAATCCAGGTATGATGCACTGTGGTGAGTTGTGTTGTGCGAGGGGTATTGCC

Reverse complement sequence

GGCAATACCCCTCGCACAACACAACTCACCACAGTGCATCATACCTGGATTATAATCACCGAGGCATGGACTCCCCAGCGACCCCCACGGATTTCTCGCC[A/G]
CTTCTCAGTCTGGCACCCCATAATGAACTATGCTATACAAAAGGTAAAGTCGTTGCCCACGCTGGCTTGTGGTTGGCACGGTTAATGTCTCATAACAGTA

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	38.90%	38.00%	3.28%	19.76%	NA
All Indica	2759	23.80%	41.20%	5.26%	29.72%	NA
All Japonica	1512	74.20%	22.40%	0.33%	3.04%	NA
Aus	269	2.20%	81.00%	0.74%	15.99%	NA
Indica I	595	29.40%	55.60%	2.52%	12.44%	NA
Indica II	465	32.30%	39.10%	3.01%	25.59%	NA
Indica III	913	14.90%	30.20%	9.42%	45.45%	NA
Indica Intermediate	786	24.90%	44.30%	3.82%	26.97%	NA
Temperate Japonica	767	84.90%	9.40%	0.65%	5.08%	NA
Tropical Japonica	504	66.70%	32.10%	0.00%	1.19%	NA
Japonica Intermediate	241	56.00%	43.60%	0.00%	0.41%	NA
VI/Aromatic	96	11.50%	66.70%	1.04%	20.83%	NA
Intermediate	90	48.90%	43.30%	2.22%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1209676708	T -> C	LOC_Os12g16870.1	upstream_gene_variant ; 1093.0bp to feature; MODIFIER	silent_mutation	Average:66.908; most accessible tissue: Minghui63 flag leaf, score: 87.326	N	N	N	N
vg1209676708	T -> C	LOC_Os12g16860.1	downstream_gene_variant ; 4675.0bp to feature; MODIFIER	silent_mutation	Average:66.908; most accessible tissue: Minghui63 flag leaf, score: 87.326	N	N	N	N
vg1209676708	T -> C	LOC_Os12g16870-LOC_Os12g16880	intergenic_region ; MODIFIER	silent_mutation	Average:66.908; most accessible tissue: Minghui63 flag leaf, score: 87.326	N	N	N	N
vg1209676708	T -> DEL	N	N	silent_mutation	Average:66.908; most accessible tissue: Minghui63 flag leaf, score: 87.326	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)
vg1209676708	T	C	0.01	0.01	0.0	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1209676708	NA	8.00E-06	mr1177	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
vg1209676708	3.66E-06	NA	mr1196	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
vg1209676708	NA	1.38E-06	mr1229	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
vg1209676708	NA	1.38E-06	mr1271	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
vg1209676708	NA	3.21E-06	mr1377	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
vg1209676708	6.60E-06	NA	mr1412	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
vg1209676708	3.43E-07	1.20E-07	mr1425	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
vg1209676708	2.59E-08	9.70E-12	mr1425	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
vg1209676708	2.36E-06	NA	mr1689	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
vg1209676708	NA	1.12E-06	mr1425_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
vg1209676708	NA	5.50E-07	mr1425_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