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Detailed information for vg0130749115:

Variant ID: vg0130749115 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 30749115
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.83, T: 0.18, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CCGCGGCTTGCTTGGAGCACTCGAACGACGGCGGCGAGAAGTCGAAGCTGCATCCCCGCGCGTGCGTGTCGTCGTCGGCGCGCGCGAGCGGCTTGTTAGT[C/T]
GGCCAGCTGTAGGAGAAGCTGCCAATGTCAGGGACGGGAGGCGAGTTGGAGTGATCCATGGCGCTGCAGCCGTGCAGTGTGCAAGGGGCAAATGGCCAAG

Reverse complement sequence

CTTGGCCATTTGCCCCTTGCACACTGCACGGCTGCAGCGCCATGGATCACTCCAACTCGCCTCCCGTCCCTGACATTGGCAGCTTCTCCTACAGCTGGCC[G/A]
ACTAACAAGCCGCTCGCGCGCGCCGACGACGACACGCACGCGCGGGGATGCAGCTTCGACTTCTCGCCGCCGTCGTTCGAGTGCTCCAAGCAAGCCGCGG

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	59.90%	39.80%	0.21%	0.00%	NA
All Indica	2759	91.60%	8.10%	0.25%	0.00%	NA
All Japonica	1512	0.90%	99.10%	0.07%	0.00%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	93.40%	6.40%	0.17%	0.00%	NA
Indica II	465	98.10%	1.70%	0.22%	0.00%	NA
Indica III	913	88.50%	11.50%	0.00%	0.00%	NA
Indica Intermediate	786	90.10%	9.30%	0.64%	0.00%	NA
Temperate Japonica	767	0.40%	99.50%	0.13%	0.00%	NA
Tropical Japonica	504	1.20%	98.80%	0.00%	0.00%	NA
Japonica Intermediate	241	1.70%	98.30%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	27.80%	70.00%	2.22%	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
vg0130749115	C -> T	LOC_Os01g53550.1	synonymous_variant ; p.Pro20Pro; LOW	synonymous_codon	Average:81.399; most accessible tissue: Minghui63 root, score: 94.021	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)
vg0130749115	C	T	0.09	0.05	0.05	0.01	0.05	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0130749115	NA	1.24E-104	mr1008	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
vg0130749115	NA	4.13E-102	mr1009	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
vg0130749115	4.01E-06	4.60E-07	mr1097	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
vg0130749115	NA	2.88E-06	mr1527	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
vg0130749115	NA	9.58E-14	mr1553	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
vg0130749115	NA	3.26E-07	mr1690	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
vg0130749115	NA	1.48E-07	mr1004_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
vg0130749115	NA	1.05E-12	mr1521_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
vg0130749115	NA	8.85E-16	mr1553_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
vg0130749115	NA	5.34E-06	mr1574_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