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Detailed information for vg1223504725:

Variant ID: vg1223504725 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23504725
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGGGCGCAGCCAGTGACGGGAAACGCCACCGCCGCGCCACGCCTCATCGCCGGGACATCTACGACCGTCACTGCTGCAGCCGTCATCGCCGTCGACCTCA[T/C]
CGGCGCCGCATCCACAACAACCGAGCGCCAACGACGACGATGGCCGACACTTCTTCATCCTCCAACACCTCAACCAGTCGGTCTATCTAAACCCTCTCCC

Reverse complement sequence

GGGAGAGGGTTTAGATAGACCGACTGGTTGAGGTGTTGGAGGATGAAGAAGTGTCGGCCATCGTCGTCGTTGGCGCTCGGTTGTTGTGGATGCGGCGCCG[A/G]
TGAGGTCGACGGCGATGACGGCTGCAGCAGTGACGGTCGTAGATGTCCCGGCGATGAGGCGTGGCGCGGCGGTGGCGTTTCCCGTCACTGGCTGCGCCCC

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	61.70%	38.10%	0.15%	0.00%	NA
All Indica	2759	97.00%	2.80%	0.18%	0.00%	NA
All Japonica	1512	1.30%	98.70%	0.00%	0.00%	NA
Aus	269	65.40%	34.20%	0.37%	0.00%	NA
Indica I	595	98.50%	1.20%	0.34%	0.00%	NA
Indica II	465	94.60%	5.40%	0.00%	0.00%	NA
Indica III	913	98.00%	2.00%	0.00%	0.00%	NA
Indica Intermediate	786	96.10%	3.60%	0.38%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.40%	98.60%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	11.50%	88.50%	0.00%	0.00%	NA
Intermediate	90	40.00%	58.90%	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
vg1223504725	T -> C	LOC_Os12g38270.1	downstream_gene_variant ; 2339.0bp to feature; MODIFIER	silent_mutation	Average:70.812; most accessible tissue: Zhenshan97 flag leaf, score: 87.846	N	N	N	N
vg1223504725	T -> C	LOC_Os12g38270.2	downstream_gene_variant ; 2339.0bp to feature; MODIFIER	silent_mutation	Average:70.812; most accessible tissue: Zhenshan97 flag leaf, score: 87.846	N	N	N	N
vg1223504725	T -> C	LOC_Os12g38280.1	intron_variant ; MODIFIER	silent_mutation	Average:70.812; most accessible tissue: Zhenshan97 flag leaf, score: 87.846	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)
vg1223504725	T	C	0.01	0.01	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
vg1223504725	NA	5.90E-16	mr1118	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
vg1223504725	NA	8.40E-15	mr1156	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
vg1223504725	NA	2.51E-18	mr1242	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
vg1223504725	NA	6.21E-11	mr1281	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
vg1223504725	NA	3.77E-08	mr1648	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
vg1223504725	5.81E-06	NA	mr1114_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
vg1223504725	1.28E-06	NA	mr1117_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
vg1223504725	3.45E-07	1.77E-18	mr1118_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
vg1223504725	3.46E-06	NA	mr1119_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
vg1223504725	NA	1.25E-15	mr1148_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
vg1223504725	2.02E-07	NA	mr1240_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
vg1223504725	3.93E-06	1.67E-24	mr1242_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
vg1223504725	NA	4.39E-23	mr1495_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
vg1223504725	6.65E-08	3.08E-15	mr1496_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