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Detailed information for vg0812088715:

Variant ID: vg0812088715 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12088715
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCGCATTCAGCTTGCGCCCAGGAACCCACCTCCGCCCGCAGCTCCCGCAGCTCCTCTAGTTCCGCCTGCAGTTCCCGCAGCTCCTGCAGCTCCAGCTCC[A/T]
GTCCCGGCTCCAGTCCCAGTGTCAGCTCCCTGCGTCCGCTCTCTCCTTCGCTCCAGCATCAGCCGCCAGGGGTCCAGCCAGTGGCAATGGAGGTTGGTTG

Reverse complement sequence

CAACCAACCTCCATTGCCACTGGCTGGACCCCTGGCGGCTGATGCTGGAGCGAAGGAGAGAGCGGACGCAGGGAGCTGACACTGGGACTGGAGCCGGGAC[T/A]
GGAGCTGGAGCTGCAGGAGCTGCGGGAACTGCAGGCGGAACTAGAGGAGCTGCGGGAGCTGCGGGCGGAGGTGGGTTCCTGGGCGCAAGCTGAATGCGCA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.90%	39.50%	4.02%	4.59%	NA
All Indica	2759	84.60%	6.40%	6.67%	2.36%	NA
All Japonica	1512	2.40%	87.90%	0.20%	9.46%	NA
Aus	269	16.70%	82.90%	0.37%	0.00%	NA
Indica I	595	97.30%	0.70%	0.50%	1.51%	NA
Indica II	465	87.30%	5.80%	4.73%	2.15%	NA
Indica III	913	78.50%	6.10%	13.36%	1.97%	NA
Indica Intermediate	786	80.40%	11.30%	4.71%	3.56%	NA
Temperate Japonica	767	2.10%	97.70%	0.00%	0.26%	NA
Tropical Japonica	504	2.00%	72.40%	0.60%	25.00%	NA
Japonica Intermediate	241	4.60%	89.20%	0.00%	6.22%	NA
VI/Aromatic	96	2.10%	91.70%	1.04%	5.21%	NA
Intermediate	90	36.70%	57.80%	1.11%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812088715	A -> T	LOC_Os08g20170.1	synonymous_variant ; p.Pro232Pro; LOW	synonymous_codon	Average:70.597; most accessible tissue: Minghui63 young leaf, score: 87.217	N	N	N	N
vg0812088715	A -> DEL	LOC_Os08g20170.1	N	frameshift_variant	Average:70.597; most accessible tissue: Minghui63 young leaf, score: 87.217	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)
vg0812088715	A	T	0.0	-0.01	-0.01	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812088715	NA	8.99E-09	mr1134	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
vg0812088715	1.61E-06	NA	mr1135	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
vg0812088715	NA	4.05E-08	mr1135	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
vg0812088715	NA	2.69E-22	mr1422	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
vg0812088715	NA	1.21E-08	mr1504	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
vg0812088715	NA	2.02E-18	mr1583	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
vg0812088715	NA	4.84E-07	mr1583	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
vg0812088715	NA	9.00E-06	mr1672	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
vg0812088715	NA	2.04E-06	mr1835	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
vg0812088715	NA	1.01E-08	mr1134_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
vg0812088715	NA	1.33E-26	mr1422_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
vg0812088715	NA	3.48E-14	mr1583_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
vg0812088715	NA	1.96E-13	mr1850_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