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Detailed information for vg0704734352:

Variant ID: vg0704734352 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 4734352
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCGGAGATACTTATACGAATTTTGCGGAAACCTGCAAACTTTGATGGACGATTGAGGCGAGTTTAGTTCTAAATTTTTTCTTCAAACTTCTAACTTTT[T/C]
CATCACATCGTTTCAATTTCAATCAAACTTCCAATGTTGACGTGAACTAAACACACCTATGAGATATGAGAAGCGGGTTGACACTTGACAAGTCCTGACA

Reverse complement sequence

TGTCAGGACTTGTCAAGTGTCAACCCGCTTCTCATATCTCATAGGTGTGTTTAGTTCACGTCAACATTGGAAGTTTGATTGAAATTGAAACGATGTGATG[A/G]
AAAAGTTAGAAGTTTGAAGAAAAAATTTAGAACTAAACTCGCCTCAATCGTCCATCAAAGTTTGCAGGTTTCCGCAAAATTCGTATAAGTATCTCCGGAA

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	78.20%	21.70%	0.04%	0.00%	NA
All Indica	2759	94.90%	5.10%	0.00%	0.00%	NA
All Japonica	1512	43.50%	56.50%	0.07%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	92.30%	7.70%	0.00%	0.00%	NA
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	93.50%	6.50%	0.00%	0.00%	NA
Indica Intermediate	786	96.30%	3.70%	0.00%	0.00%	NA
Temperate Japonica	767	10.00%	89.80%	0.13%	0.00%	NA
Tropical Japonica	504	85.90%	14.10%	0.00%	0.00%	NA
Japonica Intermediate	241	61.00%	39.00%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	9.40%	1.04%	0.00%	NA
Intermediate	90	75.60%	24.40%	0.00%	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
vg0704734352	T -> C	LOC_Os07g09060.1	upstream_gene_variant ; 274.0bp to feature; MODIFIER	silent_mutation	Average:98.499; most accessible tissue: Zhenshan97 panicle, score: 99.569	N	N	N	N
vg0704734352	T -> C	LOC_Os07g09060.2	upstream_gene_variant ; 274.0bp to feature; MODIFIER	silent_mutation	Average:98.499; most accessible tissue: Zhenshan97 panicle, score: 99.569	N	N	N	N
vg0704734352	T -> C	LOC_Os07g09060.3	upstream_gene_variant ; 274.0bp to feature; MODIFIER	silent_mutation	Average:98.499; most accessible tissue: Zhenshan97 panicle, score: 99.569	N	N	N	N
vg0704734352	T -> C	LOC_Os07g09050.1	downstream_gene_variant ; 821.0bp to feature; MODIFIER	silent_mutation	Average:98.499; most accessible tissue: Zhenshan97 panicle, score: 99.569	N	N	N	N
vg0704734352	T -> C	LOC_Os07g09050.2	downstream_gene_variant ; 1969.0bp to feature; MODIFIER	silent_mutation	Average:98.499; most accessible tissue: Zhenshan97 panicle, score: 99.569	N	N	N	N
vg0704734352	T -> C	LOC_Os07g09050-LOC_Os07g09060	intergenic_region ; MODIFIER	silent_mutation	Average:98.499; most accessible tissue: Zhenshan97 panicle, score: 99.569	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)
vg0704734352	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
vg0704734352	NA	4.64E-07	mr1252	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
vg0704734352	NA	2.25E-06	mr1330	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
vg0704734352	NA	6.78E-09	mr1746	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
vg0704734352	NA	6.23E-07	mr1748	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
vg0704734352	NA	3.06E-06	mr1837	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
vg0704734352	NA	2.80E-06	mr1063_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
vg0704734352	NA	4.55E-08	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
vg0704734352	NA	8.21E-07	mr1183_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
vg0704734352	NA	7.38E-07	mr1528_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
vg0704734352	NA	1.03E-07	mr1794_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