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Detailed information for vg0431700870:

Variant ID: vg0431700870 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31700870
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCCATCAAAAAATAACCCAAAGAAATCAAAACAAAAGCGAGCACCCACCGATGATCACTCACTGATCTCTCATCACCAAACGCCTCCGACCTCGCTCGCG[T/C]
CGCGCGCCGCGCACCCATCCCCCCGGCCTCGCCACCACCCACTCCCGATCGCCCCCGTCGCCACCCACCCCCTCAGAAATCTCATCTTTTCCGCCTCCTC

Reverse complement sequence

GAGGAGGCGGAAAAGATGAGATTTCTGAGGGGGTGGGTGGCGACGGGGGCGATCGGGAGTGGGTGGTGGCGAGGCCGGGGGGATGGGTGCGCGGCGCGCG[A/G]
CGCGAGCGAGGTCGGAGGCGTTTGGTGATGAGAGATCAGTGAGTGATCATCGGTGGGTGCTCGCTTTTGTTTTGATTTCTTTGGGTTATTTTTTGATGGA

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	62.90%	29.50%	3.47%	4.10%	NA
All Indica	2759	57.60%	29.70%	5.80%	6.96%	NA
All Japonica	1512	74.20%	25.70%	0.07%	0.00%	NA
Aus	269	60.60%	39.40%	0.00%	0.00%	NA
Indica I	595	36.30%	26.60%	17.31%	19.83%	NA
Indica II	465	74.60%	22.60%	1.08%	1.72%	NA
Indica III	913	63.40%	32.40%	1.64%	2.52%	NA
Indica Intermediate	786	56.70%	33.10%	4.71%	5.47%	NA
Temperate Japonica	767	90.00%	9.90%	0.13%	0.00%	NA
Tropical Japonica	504	63.30%	36.70%	0.00%	0.00%	NA
Japonica Intermediate	241	46.90%	53.10%	0.00%	0.00%	NA
VI/Aromatic	96	37.50%	61.50%	1.04%	0.00%	NA
Intermediate	90	70.00%	25.60%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0431700870	T -> C	LOC_Os04g53230.1	upstream_gene_variant ; 37.0bp to feature; MODIFIER	silent_mutation	Average:95.578; most accessible tissue: Minghui63 flag leaf, score: 99.02	N	N	N	N
vg0431700870	T -> C	LOC_Os04g53214.2	downstream_gene_variant ; 4223.0bp to feature; MODIFIER	silent_mutation	Average:95.578; most accessible tissue: Minghui63 flag leaf, score: 99.02	N	N	N	N
vg0431700870	T -> C	LOC_Os04g53220.1	downstream_gene_variant ; 581.0bp to feature; MODIFIER	silent_mutation	Average:95.578; most accessible tissue: Minghui63 flag leaf, score: 99.02	N	N	N	N
vg0431700870	T -> C	LOC_Os04g53214.1	downstream_gene_variant ; 4225.0bp to feature; MODIFIER	silent_mutation	Average:95.578; most accessible tissue: Minghui63 flag leaf, score: 99.02	N	N	N	N
vg0431700870	T -> C	LOC_Os04g53220-LOC_Os04g53230	intergenic_region ; MODIFIER	silent_mutation	Average:95.578; most accessible tissue: Minghui63 flag leaf, score: 99.02	N	N	N	N
vg0431700870	T -> DEL	N	N	silent_mutation	Average:95.578; most accessible tissue: Minghui63 flag leaf, score: 99.02	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)
vg0431700870	T	C	-0.06	-0.05	-0.03	-0.01	-0.03	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431700870	NA	2.24E-17	Plant_height	All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0431700870	NA	1.35E-07	mr1249	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
vg0431700870	NA	9.69E-06	mr1788	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