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Detailed information for vg0608826344:

Variant ID: vg0608826344 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8826344
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 96. )

Flanking Sequence (100 bp) in Reference Genome:

TGGAACCTCTACCTCGACGAGCCCGCCGCCGTGTGGGCGCCGCACGTCCCGGCGTTCGACTACGCCGTCGTGTCGGCGTCGAGCTGGTTCTACCGGCCGT[C/A]
GATGCTGTACGAGGCCGGCCGGCTCGTCGGGTGCCACCACTGCCTCCTCCCCAACGTCACCGACCTCACGCTGCGGTACGCGCTCCGCATGGCCACCCGC

Reverse complement sequence

GCGGGTGGCCATGCGGAGCGCGTACCGCAGCGTGAGGTCGGTGACGTTGGGGAGGAGGCAGTGGTGGCACCCGACGAGCCGGCCGGCCTCGTACAGCATC[G/T]
ACGGCCGGTAGAACCAGCTCGACGCCGACACGACGGCGTAGTCGAACGCCGGGACGTGCGGCGCCCACACGGCGGCGGGCTCGTCGAGGTAGAGGTTCCA

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	62.90%	36.90%	0.17%	0.00%	NA
All Indica	2759	38.30%	61.40%	0.25%	0.00%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	46.70%	53.30%	0.00%	0.00%	NA
Indica II	465	19.40%	80.40%	0.22%	0.00%	NA
Indica III	913	50.40%	49.30%	0.33%	0.00%	NA
Indica Intermediate	786	29.30%	70.40%	0.38%	0.00%	NA
Temperate Japonica	767	99.00%	1.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	60.00%	38.90%	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
vg0608826344	C -> A	LOC_Os06g15560.1	5_prime_UTR_variant ; 2.0bp to feature; MODIFIER	silent_mutation	Average:82.115; most accessible tissue: Zhenshan97 panicle, score: 93.936	N	N	N	N
vg0608826344	C -> A	LOC_Os06g15550.1	downstream_gene_variant ; 3201.0bp to feature; MODIFIER	silent_mutation	Average:82.115; most accessible tissue: Zhenshan97 panicle, score: 93.936	N	N	N	N
vg0608826344	C -> A	LOC_Os06g15570.1	downstream_gene_variant ; 645.0bp to feature; MODIFIER	silent_mutation	Average:82.115; most accessible tissue: Zhenshan97 panicle, score: 93.936	N	N	N	N
vg0608826344	C -> A	LOC_Os06g15570.2	downstream_gene_variant ; 645.0bp to feature; MODIFIER	silent_mutation	Average:82.115; most accessible tissue: Zhenshan97 panicle, score: 93.936	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)
vg0608826344	C	A	0.01	0.0	0.01	0.01	0.02	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608826344	NA	9.89E-07	mr1157	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
vg0608826344	NA	1.60E-08	mr1446	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
vg0608826344	NA	6.07E-07	mr1570	Ind_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
vg0608826344	NA	2.02E-07	mr1989	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
vg0608826344	NA	8.00E-06	mr1329_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
vg0608826344	NA	4.47E-12	mr1377_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
vg0608826344	NA	4.29E-07	mr1446_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
vg0608826344	NA	8.50E-06	mr1524_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
vg0608826344	NA	2.83E-06	mr1570_2	Ind_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
vg0608826344	NA	3.41E-09	mr1649_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
vg0608826344	NA	2.80E-06	mr1668_2	Ind_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
vg0608826344	NA	7.13E-07	mr1754_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