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Detailed information for vg0621761253:

Variant ID: vg0621761253 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21761253
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGTTAGAAGCTTCCAAAGAAAAAAAAATCCCACGCCTCCAAACGCCCAAAATGCATCTCCCCTCGCCTTCCTCTAGTACCTTCCAGAATGTTCCGTTTC[C/T]
CTCCTATAAATTACAAAATCCCACCTTCTTCTCCCGCCAAAAGCACGCCGATGGACTACTCGACGGTGAAGCAGGAGGAGGTGGAGGTGGTGGTGCTGGA

Reverse complement sequence

TCCAGCACCACCACCTCCACCTCCTCCTGCTTCACCGTCGAGTAGTCCATCGGCGTGCTTTTGGCGGGAGAAGAAGGTGGGATTTTGTAATTTATAGGAG[G/A]
GAAACGGAACATTCTGGAAGGTACTAGAGGAAGGCGAGGGGAGATGCATTTTGGGCGTTTGGAGGCGTGGGATTTTTTTTTCTTTGGAAGCTTCTAACGT

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	70.40%	4.00%	18.85%	6.73%	NA
All Indica	2759	78.70%	0.60%	17.76%	2.90%	NA
All Japonica	1512	66.10%	11.30%	13.76%	8.80%	NA
Aus	269	6.70%	0.00%	59.48%	33.83%	NA
Indica I	595	83.50%	0.00%	15.13%	1.34%	NA
Indica II	465	79.80%	0.60%	16.56%	3.01%	NA
Indica III	913	74.40%	0.10%	21.91%	3.61%	NA
Indica Intermediate	786	79.50%	1.70%	15.65%	3.18%	NA
Temperate Japonica	767	76.40%	3.40%	8.47%	11.73%	NA
Tropical Japonica	504	58.30%	13.90%	21.23%	6.55%	NA
Japonica Intermediate	241	49.80%	31.10%	14.94%	4.15%	NA
VI/Aromatic	96	70.80%	0.00%	17.71%	11.46%	NA
Intermediate	90	75.60%	3.30%	17.78%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0621761253	C -> T	LOC_Os06g36920.1	upstream_gene_variant ; 2689.0bp to feature; MODIFIER	silent_mutation	Average:92.589; most accessible tissue: Zhenshan97 root, score: 97.757	N	N	N	N
vg0621761253	C -> T	LOC_Os06g36930.1	upstream_gene_variant ; 51.0bp to feature; MODIFIER	silent_mutation	Average:92.589; most accessible tissue: Zhenshan97 root, score: 97.757	N	N	N	N
vg0621761253	C -> T	LOC_Os06g36940.1	downstream_gene_variant ; 1865.0bp to feature; MODIFIER	silent_mutation	Average:92.589; most accessible tissue: Zhenshan97 root, score: 97.757	N	N	N	N
vg0621761253	C -> T	LOC_Os06g36950.1	downstream_gene_variant ; 4561.0bp to feature; MODIFIER	silent_mutation	Average:92.589; most accessible tissue: Zhenshan97 root, score: 97.757	N	N	N	N
vg0621761253	C -> T	LOC_Os06g36920-LOC_Os06g36930	intergenic_region ; MODIFIER	silent_mutation	Average:92.589; most accessible tissue: Zhenshan97 root, score: 97.757	N	N	N	N
vg0621761253	C -> DEL	N	N	silent_mutation	Average:92.589; most accessible tissue: Zhenshan97 root, score: 97.757	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)
vg0621761253	C	T	-0.02	-0.04	-0.05	-0.03	-0.04	-0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621761253	NA	1.20E-06	mr1113	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
vg0621761253	NA	2.85E-06	mr1114	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
vg0621761253	NA	1.41E-07	mr1117	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
vg0621761253	8.27E-07	NA	mr1182	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
vg0621761253	NA	8.86E-06	mr1182	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
vg0621761253	5.46E-06	NA	mr1240	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
vg0621761253	NA	1.37E-08	mr1240	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
vg0621761253	3.88E-06	NA	mr1282	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
vg0621761253	NA	7.10E-08	mr1408	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
vg0621761253	NA	2.92E-08	mr1691	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
vg0621761253	NA	7.41E-08	mr1961	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
vg0621761253	NA	6.10E-07	mr1691_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
vg0621761253	NA	6.09E-09	mr1821_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
vg0621761253	NA	7.10E-06	mr1923_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