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Detailed information for vg0919019906:

Variant ID: vg0919019906 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 19019906
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCAAGAGAAGAAATATCTACTTGTCCCTCACACATACTCTCTCCATTAAAAAAAAAGACAATCTAGAGGATCGTCTCGGATTGTCTCTTCCTAGTACAA[C/T]
GAATTTAAACAACACTTTATCCAGATTTGTTATGAAGGGGTCACATTTTTTTCTAGATTTTTTTTTCCTGAGGAGTCATAATATATTATCCAAGAATGCT

Reverse complement sequence

AGCATTCTTGGATAATATATTATGACTCCTCAGGAAAAAAAAATCTAGAAAAAAATGTGACCCCTTCATAACAAATCTGGATAAAGTGTTGTTTAAATTC[G/A]
TTGTACTAGGAAGAGACAATCCGAGACGATCCTCTAGATTGTCTTTTTTTTTAATGGAGAGAGTATGTGTGAGGGACAAGTAGATATTTCTTCTCTTGCC

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	39.50%	4.10%	8.51%	47.97%	NA
All Indica	2759	10.80%	0.40%	13.16%	75.68%	NA
All Japonica	1512	88.10%	11.80%	0.13%	0.00%	NA
Aus	269	29.00%	0.00%	11.90%	59.11%	NA
Indica I	595	7.90%	0.00%	22.35%	69.75%	NA
Indica II	465	12.90%	0.00%	5.59%	81.51%	NA
Indica III	913	9.40%	1.00%	11.61%	77.98%	NA
Indica Intermediate	786	13.40%	0.10%	12.47%	74.05%	NA
Temperate Japonica	767	99.50%	0.40%	0.13%	0.00%	NA
Tropical Japonica	504	73.60%	26.40%	0.00%	0.00%	NA
Japonica Intermediate	241	82.20%	17.40%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	71.10%	4.40%	4.44%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0919019906	C -> DEL	N	N	silent_mutation	Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631	N	N	N	N
vg0919019906	C -> T	LOC_Os09g31506.1	upstream_gene_variant ; 1152.0bp to feature; MODIFIER	silent_mutation	Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631	N	N	N	N
vg0919019906	C -> T	LOC_Os09g31514.1	downstream_gene_variant ; 514.0bp to feature; MODIFIER	silent_mutation	Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631	N	N	N	N
vg0919019906	C -> T	LOC_Os09g31514.2	downstream_gene_variant ; 514.0bp to feature; MODIFIER	silent_mutation	Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631	N	N	N	N
vg0919019906	C -> T	LOC_Os09g31514.4	downstream_gene_variant ; 514.0bp to feature; MODIFIER	silent_mutation	Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631	N	N	N	N
vg0919019906	C -> T	LOC_Os09g31514.3	downstream_gene_variant ; 2230.0bp to feature; MODIFIER	silent_mutation	Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631	N	N	N	N
vg0919019906	C -> T	LOC_Os09g31506-LOC_Os09g31514	intergenic_region ; MODIFIER	silent_mutation	Average:74.188; most accessible tissue: Minghui63 flag leaf, score: 93.631	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)
vg0919019906	C	T	-0.04	-0.11	-0.08	-0.05	-0.07	-0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0919019906	NA	3.17E-09	mr1022	Jap_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
vg0919019906	NA	9.73E-06	mr1225	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
vg0919019906	NA	5.15E-06	mr1232_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
vg0919019906	NA	9.35E-07	mr1557_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
vg0919019906	NA	3.50E-07	mr1905_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
vg0919019906	NA	3.61E-07	mr1944_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