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Detailed information for vg0421834990:

Variant ID: vg0421834990 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21834990
Reference Allele: C	Alternative Allele: G
Primary Allele: G	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TATAATCTTGATCAAATTGACCAATAAAAATACATTTAATATAATATAAAACGGAGGGTGCAGCAGTTTTTCGGTTGGTCCTCCTGCGGTGCCGGTCGAT[C/G]
GAGACGAAAAGAGGGGGGGGGGGGGGGGGGTACGTTAGTTAGCCGTAGCTGTCTGTTCCGTCGCAACGGGCTTTGGCGAGGTAGCCACGGCGGCTACAGC

Reverse complement sequence

GCTGTAGCCGCCGTGGCTACCTCGCCAAAGCCCGTTGCGACGGAACAGACAGCTACGGCTAACTAACGTACCCCCCCCCCCCCCCCCCTCTTTTCGTCTC[G/C]
ATCGACCGGCACCGCAGGAGGACCAACCGAAAAACTGCTGCACCCTCCGTTTTATATTATATTAAATGTATTTTTATTGGTCAATTTGATCAAGATTATA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.00%	5.90%	4.10%	0.97%	NA
All Indica	2759	96.60%	0.50%	2.17%	0.76%	NA
All Japonica	1512	74.10%	17.30%	6.88%	1.65%	NA
Aus	269	91.80%	0.40%	7.81%	0.00%	NA
Indica I	595	93.60%	1.20%	5.04%	0.17%	NA
Indica II	465	93.10%	0.90%	3.66%	2.37%	NA
Indica III	913	98.90%	0.10%	0.33%	0.66%	NA
Indica Intermediate	786	98.20%	0.10%	1.27%	0.38%	NA
Temperate Japonica	767	58.00%	30.80%	9.26%	1.96%	NA
Tropical Japonica	504	94.00%	1.40%	3.97%	0.60%	NA
Japonica Intermediate	241	83.80%	7.90%	5.39%	2.90%	NA
VI/Aromatic	96	96.90%	0.00%	3.12%	0.00%	NA
Intermediate	90	88.90%	4.40%	6.67%	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
vg0421834990	C -> DEL	N	N	silent_mutation	Average:97.807; most accessible tissue: Zhenshan97 flower, score: 99.373	N	N	N	N
vg0421834990	C -> G	LOC_Os04g35830.1	upstream_gene_variant ; 921.0bp to feature; MODIFIER	silent_mutation	Average:97.807; most accessible tissue: Zhenshan97 flower, score: 99.373	N	N	N	N
vg0421834990	C -> G	LOC_Os04g35820.1	downstream_gene_variant ; 4741.0bp to feature; MODIFIER	silent_mutation	Average:97.807; most accessible tissue: Zhenshan97 flower, score: 99.373	N	N	N	N
vg0421834990	C -> G	LOC_Os04g35820-LOC_Os04g35830	intergenic_region ; MODIFIER	silent_mutation	Average:97.807; most accessible tissue: Zhenshan97 flower, score: 99.373	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)
vg0421834990	C	G	0.06	0.13	0.09	0.1	0.06	0.06

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421834990	NA	1.62E-06	mr1045	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
vg0421834990	2.02E-06	2.50E-08	mr1252	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
vg0421834990	NA	5.95E-06	mr1844	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
vg0421834990	NA	1.11E-06	mr1182_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