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Detailed information for vg0218948347:

Variant ID: vg0218948347 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 18948347
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

TAAGCCATACACGGAGTATGTAATTAACCCCTCGGACACGCCCCCGCGTTCCACAGCGATCGCCGACGTCGATCGAGATCATGGGCGCGTTGCTATATCA[T/C]
GTTCGATGGAAAAAAAAACAGAAACAAAACCTCGCAAATTTCAAACCTTAATTTATATCCACTTAACGATTCGTGCTTAATTTAGGATGTCTTCGGAACC

Reverse complement sequence

GGTTCCGAAGACATCCTAAATTAAGCACGAATCGTTAAGTGGATATAAATTAAGGTTTGAAATTTGCGAGGTTTTGTTTCTGTTTTTTTTTCCATCGAAC[A/G]
TGATATAGCAACGCGCCCATGATCTCGATCGACGTCGGCGATCGCTGTGGAACGCGGGGGCGTGTCCGAGGGGTTAATTACATACTCCGTGTATGGCTTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	75.30%	24.10%	0.61%	0.00%	NA
All Indica	2759	88.40%	11.50%	0.04%	0.00%	NA
All Japonica	1512	62.60%	35.60%	1.79%	0.00%	NA
Aus	269	34.20%	65.80%	0.00%	0.00%	NA
Indica I	595	70.40%	29.40%	0.17%	0.00%	NA
Indica II	465	95.50%	4.50%	0.00%	0.00%	NA
Indica III	913	96.90%	3.10%	0.00%	0.00%	NA
Indica Intermediate	786	88.00%	12.00%	0.00%	0.00%	NA
Temperate Japonica	767	41.70%	54.90%	3.39%	0.00%	NA
Tropical Japonica	504	96.60%	3.40%	0.00%	0.00%	NA
Japonica Intermediate	241	57.70%	41.90%	0.41%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	73.30%	25.60%	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
vg0218948347	T -> C	LOC_Os02g32060-LOC_Os02g32070	intergenic_region ; MODIFIER	silent_mutation	Average:85.181; most accessible tissue: Minghui63 root, score: 98.781	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)
vg0218948347	T	C	0.07	0.03	0.04	0.01	0.04	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0218948347	NA	7.97E-07	mr1192	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
vg0218948347	NA	9.80E-06	mr1201	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
vg0218948347	NA	8.51E-07	mr1274	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
vg0218948347	NA	1.54E-09	mr1585	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
vg0218948347	NA	9.15E-07	mr1126_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
vg0218948347	NA	1.21E-10	mr1585_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
vg0218948347	NA	3.50E-07	mr1608_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
vg0218948347	NA	2.42E-09	mr1780_2	Jap_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
vg0218948347	NA	1.09E-13	mr1914_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
vg0218948347	NA	4.92E-06	mr1914_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