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Detailed information for vg1012891999:

Variant ID: vg1012891999 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12891999
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCTTCAAAACAAATCTACAAAGATTAGTTTAGCTCTAGCTTCTTGAAAGTAAATACCGAAATGAACTCCTTACGTAAAAAAAAAAGAAATATATATACAA[A/C]
GATAATAAGCGGATGGATGTGGTGGCGAGAGAAACCTCTAGAGCCATGCAAAAAAAATGCTTAATTAGCTTCCCATGAACGCCTTGCGGATCTCGGCGAC

Reverse complement sequence

GTCGCCGAGATCCGCAAGGCGTTCATGGGAAGCTAATTAAGCATTTTTTTTGCATGGCTCTAGAGGTTTCTCTCGCCACCACATCCATCCGCTTATTATC[T/G]
TTGTATATATATTTCTTTTTTTTTTACGTAAGGAGTTCATTTCGGTATTTACTTTCAAGAAGCTAGAGCTAAACTAATCTTTGTAGATTTGTTTTGAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.90%	2.80%	6.67%	4.59%	NA
All Indica	2759	78.30%	4.00%	10.08%	7.65%	NA
All Japonica	1512	97.80%	0.50%	1.46%	0.20%	NA
Aus	269	93.70%	3.70%	2.60%	0.00%	NA
Indica I	595	74.10%	2.70%	16.81%	6.39%	NA
Indica II	465	76.60%	4.70%	8.60%	10.11%	NA
Indica III	913	82.70%	3.70%	6.46%	7.12%	NA
Indica Intermediate	786	77.20%	5.00%	10.05%	7.76%	NA
Temperate Japonica	767	99.30%	0.10%	0.39%	0.13%	NA
Tropical Japonica	504	96.20%	0.80%	2.78%	0.20%	NA
Japonica Intermediate	241	96.30%	1.20%	2.07%	0.41%	NA
VI/Aromatic	96	90.60%	4.20%	4.17%	1.04%	NA
Intermediate	90	92.20%	1.10%	4.44%	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
vg1012891999	A -> C	LOC_Os10g25040.2	3_prime_UTR_variant ; 65.0bp to feature; MODIFIER	silent_mutation	Average:94.018; most accessible tissue: Minghui63 young leaf, score: 96.882	N	N	N	N
vg1012891999	A -> C	LOC_Os10g25040.1	3_prime_UTR_variant ; 65.0bp to feature; MODIFIER	silent_mutation	Average:94.018; most accessible tissue: Minghui63 young leaf, score: 96.882	N	N	N	N
vg1012891999	A -> C	LOC_Os10g25030.1	upstream_gene_variant ; 3697.0bp to feature; MODIFIER	silent_mutation	Average:94.018; most accessible tissue: Minghui63 young leaf, score: 96.882	N	N	N	N
vg1012891999	A -> DEL	N	N	silent_mutation	Average:94.018; most accessible tissue: Minghui63 young leaf, score: 96.882	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)
vg1012891999	A	C	0.0	0.0	-0.01	-0.01	-0.01	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012891999	4.04E-08	1.77E-07	mr1305_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
vg1012891999	9.84E-06	NA	mr1480_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
vg1012891999	9.71E-06	NA	mr1765_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
vg1012891999	1.47E-07	1.47E-07	mr1765_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