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Detailed information for vg0821172360:

Variant ID: vg0821172360 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 21172360
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGTCCTCCGCCAGACCCAACGGGTCGAACCCGTTATCGCCTGGCAAGCTGTACACACCCGTTTAACTATCGTGTTAGTAGTTTTTTTATGATGCTCTC[T/C]
ACTGGTAGTAGAAATATATTTTTTTTATGTGTGTGCTCACCTGCCGTTGAGGTAGGTGGGAGAAGGGAGGCCGGGGAGCCACTCTCCCTTGGCCTCCGCC

Reverse complement sequence

GGCGGAGGCCAAGGGAGAGTGGCTCCCCGGCCTCCCTTCTCCCACCTACCTCAACGGCAGGTGAGCACACACATAAAAAAAATATATTTCTACTACCAGT[A/G]
GAGAGCATCATAAAAAAACTACTAACACGATAGTTAAACGGGTGTGTACAGCTTGCCAGGCGATAACGGGTTCGACCCGTTGGGTCTGGCGGAGGACCCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.00%	9.00%	0.00%	0.00%	NA
All Indica	2759	96.00%	4.00%	0.00%	0.00%	NA
All Japonica	1512	79.70%	20.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.10%	2.90%	0.00%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	94.00%	6.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.80%	3.20%	0.00%	0.00%	NA
Temperate Japonica	767	97.40%	2.60%	0.00%	0.00%	NA
Tropical Japonica	504	53.80%	46.20%	0.00%	0.00%	NA
Japonica Intermediate	241	77.60%	22.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	11.10%	0.00%	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
vg0821172360	T -> C	LOC_Os08g33810.1	upstream_gene_variant ; 2601.0bp to feature; MODIFIER	silent_mutation	Average:96.908; most accessible tissue: Zhenshan97 panicle, score: 99.287	N	N	N	N
vg0821172360	T -> C	LOC_Os08g33830.1	downstream_gene_variant ; 1058.0bp to feature; MODIFIER	silent_mutation	Average:96.908; most accessible tissue: Zhenshan97 panicle, score: 99.287	N	N	N	N
vg0821172360	T -> C	LOC_Os08g33830.2	downstream_gene_variant ; 1058.0bp to feature; MODIFIER	silent_mutation	Average:96.908; most accessible tissue: Zhenshan97 panicle, score: 99.287	N	N	N	N
vg0821172360	T -> C	LOC_Os08g33820.1	intron_variant ; MODIFIER	silent_mutation	Average:96.908; most accessible tissue: Zhenshan97 panicle, score: 99.287	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)
vg0821172360	T	C	-0.03	-0.02	-0.02	-0.02	-0.02	-0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0821172360	NA	2.89E-18	mr1301	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
vg0821172360	NA	3.72E-17	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
vg0821172360	NA	3.86E-14	mr1410	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
vg0821172360	2.76E-06	NA	mr1486	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
vg0821172360	4.24E-06	5.80E-06	mr1588	Ind_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
vg0821172360	NA	4.39E-18	mr1699	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
vg0821172360	NA	8.41E-07	mr1951	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
vg0821172360	NA	7.64E-13	mr1980	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
vg0821172360	NA	5.09E-17	mr1301_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
vg0821172360	NA	1.26E-13	mr1410_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
vg0821172360	NA	1.34E-12	mr1533_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
vg0821172360	3.73E-06	NA	mr1588_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
vg0821172360	NA	4.17E-07	mr1668_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
vg0821172360	NA	3.41E-08	mr1746_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