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Detailed information for vg0137820754:

Variant ID: vg0137820754 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 37820754
Reference Allele: C	Alternative Allele: A
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, A: 0.19, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CAAAGGTTGTGGTTCGGCAGCTAGCTACTTATGTAGCCACTATAGTCCTAGGTCAGCCCATCTGATTAGATAGAGTGCACTCAGTCCCTTCCCCTACTTC[C/A]
TCTTTTTTTTTTTCTGTTCAGTTGTAATTGGCAACTTTACTCGTCTTATTGCAAAGATATGTAAGTCTTTTACGTATTAAAAAATTGCTCGCGAGCTTTG

Reverse complement sequence

CAAAGCTCGCGAGCAATTTTTTAATACGTAAAAGACTTACATATCTTTGCAATAAGACGAGTAAAGTTGCCAATTACAACTGAACAGAAAAAAAAAAAGA[G/T]
GAAGTAGGGGAAGGGACTGAGTGCACTCTATCTAATCAGATGGGCTGACCTAGGACTATAGTGGCTACATAAGTAGCTAGCTGCCGAACCACAACCTTTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	46.90%	39.10%	6.71%	7.30%	NA
All Indica	2759	68.20%	8.30%	11.09%	12.40%	NA
All Japonica	1512	2.40%	97.40%	0.13%	0.07%	NA
Aus	269	99.30%	0.40%	0.37%	0.00%	NA
Indica I	595	62.40%	6.40%	16.97%	14.29%	NA
Indica II	465	84.10%	3.40%	8.39%	4.09%	NA
Indica III	913	60.20%	11.70%	10.51%	17.52%	NA
Indica Intermediate	786	72.50%	8.70%	8.91%	9.92%	NA
Temperate Japonica	767	2.20%	97.50%	0.13%	0.13%	NA
Tropical Japonica	504	2.20%	97.60%	0.20%	0.00%	NA
Japonica Intermediate	241	3.30%	96.70%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	31.10%	57.80%	8.89%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0137820754	C -> A	LOC_Os01g65169.1	upstream_gene_variant ; 464.0bp to feature; MODIFIER	silent_mutation	Average:68.788; most accessible tissue: Callus, score: 94.92	N	N	N	N
vg0137820754	C -> A	LOC_Os01g65150.1	downstream_gene_variant ; 3979.0bp to feature; MODIFIER	silent_mutation	Average:68.788; most accessible tissue: Callus, score: 94.92	N	N	N	N
vg0137820754	C -> A	LOC_Os01g65150-LOC_Os01g65169	intergenic_region ; MODIFIER	silent_mutation	Average:68.788; most accessible tissue: Callus, score: 94.92	N	N	N	N
vg0137820754	C -> DEL	N	N	silent_mutation	Average:68.788; most accessible tissue: Callus, score: 94.92	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)
vg0137820754	C	A	0.02	0.0	-0.01	-0.01	-0.01	-0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0137820754	NA	3.82E-13	mr1170	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
vg0137820754	3.13E-09	2.24E-35	mr1375	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
vg0137820754	1.47E-06	1.11E-08	mr1375	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
vg0137820754	3.89E-22	7.74E-90	mr1517	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
vg0137820754	1.45E-17	2.71E-21	mr1517	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
vg0137820754	2.07E-18	9.92E-72	mr1538	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
vg0137820754	8.24E-12	7.84E-15	mr1538	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
vg0137820754	NA	1.12E-07	mr1170_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
vg0137820754	1.16E-25	NA	mr1517_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
vg0137820754	2.65E-20	7.69E-23	mr1517_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
vg0137820754	1.10E-20	NA	mr1538_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
vg0137820754	3.52E-14	2.36E-21	mr1538_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