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Detailed information for vg0430855895:

Variant ID: vg0430855895 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30855895
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CAAAGCGGTGGATGGAGAGAACGAGCGATGAAATGGAGGAGAAGAAGCCAAAGTCAAAGCCAAAAGCCAAAAGTCAAAGTGTGTCTCGAATTCATGGATG[C/T]
GGAAAAATTAGCTCTAAATCCTCCCAGATTCCAGAGATAAGCGCGTGGTTTGAGGATTTTGCCAGCCTTGAATTGAAAGCGCAGTTTTAGACAATTTCTT

Reverse complement sequence

AAGAAATTGTCTAAAACTGCGCTTTCAATTCAAGGCTGGCAAAATCCTCAAACCACGCGCTTATCTCTGGAATCTGGGAGGATTTAGAGCTAATTTTTCC[G/A]
CATCCATGAATTCGAGACACACTTTGACTTTTGGCTTTTGGCTTTGACTTTGGCTTCTTCTCCTCCATTTCATCGCTCGTTCTCTCCATCCACCGCTTTG

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	91.80%	8.10%	0.11%	0.00%	NA
All Indica	2759	99.40%	0.60%	0.00%	0.00%	NA
All Japonica	1512	78.00%	21.70%	0.26%	0.00%	NA
Aus	269	90.00%	10.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.60%	0.40%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	1.10%	0.00%	0.00%	NA
Temperate Japonica	767	98.60%	1.40%	0.00%	0.00%	NA
Tropical Japonica	504	41.90%	57.50%	0.60%	0.00%	NA
Japonica Intermediate	241	88.40%	11.20%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	13.30%	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
vg0430855895	C -> T	LOC_Os04g51970.1	5_prime_UTR_variant ; 1999.0bp to feature; MODIFIER	silent_mutation	Average:97.918; most accessible tissue: Minghui63 flower, score: 99.015	N	N	N	N
vg0430855895	C -> T	LOC_Os04g51970.2	5_prime_UTR_variant ; 1999.0bp to feature; MODIFIER	silent_mutation	Average:97.918; most accessible tissue: Minghui63 flower, score: 99.015	N	N	N	N
vg0430855895	C -> T	LOC_Os04g51980.1	upstream_gene_variant ; 4712.0bp to feature; MODIFIER	silent_mutation	Average:97.918; most accessible tissue: Minghui63 flower, score: 99.015	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)
vg0430855895	C	T	-0.01	0.0	-0.01	-0.02	-0.02	-0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430855895	NA	1.61E-08	mr1248	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
vg0430855895	2.33E-06	NA	mr1301	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
vg0430855895	4.13E-10	NA	mr1745	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
vg0430855895	NA	6.79E-08	mr1090_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
vg0430855895	NA	4.74E-06	mr1211_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
vg0430855895	NA	3.87E-07	mr1321_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
vg0430855895	NA	1.48E-08	mr1696_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
vg0430855895	2.84E-20	NA	mr1745_2	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
vg0430855895	8.86E-09	4.03E-06	mr1745_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