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Detailed information for vg0503312521:

Variant ID: vg0503312521 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 3312521
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAGCCACCCGGATGGCGTCGTGGCGGGGGTTGCAGCTCGGGCGCCGCCGACGGCGGCGGAGCTAGGGTTTTGGGGGGTTTGCTTCGCGTGGACGCTAGGG[C/A]
TTGCGCCGCCGCGGGCCACCAACTGCGGGGAGTGGAGTGGTGGGTGGGTGGGGGACGAAGCGGAGATTTGTGAGCGACGGGGAAAATGGGGAGAGGATTG

Reverse complement sequence

CAATCCTCTCCCCATTTTCCCCGTCGCTCACAAATCTCCGCTTCGTCCCCCACCCACCCACCACTCCACTCCCCGCAGTTGGTGGCCCGCGGCGGCGCAA[G/T]
CCCTAGCGTCCACGCGAAGCAAACCCCCCAAAACCCTAGCTCCGCCGCCGTCGGCGGCGCCCGAGCTGCAACCCCCGCCACGACGCCATCCGGGTGGCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.00%	2.30%	0.44%	0.21%	NA
All Indica	2759	99.90%	0.00%	0.04%	0.00%	NA
All Japonica	1512	91.30%	6.70%	1.26%	0.66%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.90%	0.10%	0.00%	0.00%	NA
Temperate Japonica	767	91.90%	4.70%	2.09%	1.30%	NA
Tropical Japonica	504	95.60%	4.20%	0.20%	0.00%	NA
Japonica Intermediate	241	80.50%	18.70%	0.83%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg0503312521	C -> DEL	N	N	silent_mutation	Average:91.415; most accessible tissue: Zhenshan97 panicle, score: 95.381	N	N	N	N
vg0503312521	C -> A	LOC_Os05g06450.1	5_prime_UTR_variant ; 153.0bp to feature; MODIFIER	silent_mutation	Average:91.415; most accessible tissue: Zhenshan97 panicle, score: 95.381	N	N	N	N
vg0503312521	C -> A	LOC_Os05g06450.2	5_prime_UTR_variant ; 153.0bp to feature; MODIFIER	silent_mutation	Average:91.415; most accessible tissue: Zhenshan97 panicle, score: 95.381	N	N	N	N
vg0503312521	C -> A	LOC_Os05g06440.1	downstream_gene_variant ; 4808.0bp to feature; MODIFIER	silent_mutation	Average:91.415; most accessible tissue: Zhenshan97 panicle, score: 95.381	N	N	N	N
vg0503312521	C -> A	LOC_Os05g06460.1	downstream_gene_variant ; 870.0bp to feature; MODIFIER	silent_mutation	Average:91.415; most accessible tissue: Zhenshan97 panicle, score: 95.381	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)
vg0503312521	C	A	-0.04	-0.05	-0.05	-0.03	-0.03	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0503312521	NA	6.08E-06	mr1071	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
vg0503312521	NA	2.18E-06	mr1140	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
vg0503312521	NA	3.04E-06	mr1613	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
vg0503312521	NA	3.59E-06	mr1618	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
vg0503312521	NA	1.85E-07	mr1913	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
vg0503312521	2.40E-06	8.31E-10	mr1071_2	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
vg0503312521	4.25E-06	5.03E-09	mr1080_2	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
vg0503312521	5.53E-06	6.15E-09	mr1100_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
vg0503312521	6.73E-06	4.01E-10	mr1203_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
vg0503312521	2.86E-07	1.87E-10	mr1402_2	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
vg0503312521	5.92E-08	9.78E-12	mr1613_2	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
vg0503312521	4.35E-06	2.48E-08	mr1619_2	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
vg0503312521	2.39E-08	1.29E-10	mr1795_2	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
vg0503312521	NA	5.40E-09	mr1913_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
vg0503312521	9.74E-07	5.73E-10	mr1962_2	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