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Detailed information for vg0725407361:

Variant ID: vg0725407361 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 25407361
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGGTACTTGGCAGTATTGCCGGTCGTATTGCTGAAGCACTACTCCCTCCGTCAAAAAAAAAAAACAAACCCTGATTTCCGTGTCCAATGTTTGACCGT[C/T]
CGTCTTATTTGAAAAAATTATGAAAAAAATTAAAAAGACAAGTCACGCTTAAAATATTAATCATGTTTTATCATCTAACAACAATGAAAATACAAATTAT

Reverse complement sequence

ATAATTTGTATTTTCATTGTTGTTAGATGATAAAACATGATTAATATTTTAAGCGTGACTTGTCTTTTTAATTTTTTTCATAATTTTTTCAAATAAGACG[G/A]
ACGGTCAAACATTGGACACGGAAATCAGGGTTTGTTTTTTTTTTTTGACGGAGGGAGTAGTGCTTCAGCAATACGACCGGCAATACTGCCAAGTACCATT

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	92.30%	4.40%	1.33%	2.01%	NA
All Indica	2759	97.00%	2.60%	0.25%	0.18%	NA
All Japonica	1512	87.40%	3.40%	3.24%	5.89%	NA
Aus	269	97.80%	1.90%	0.37%	0.00%	NA
Indica I	595	94.10%	5.90%	0.00%	0.00%	NA
Indica II	465	96.60%	0.90%	1.51%	1.08%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	96.20%	3.80%	0.00%	0.00%	NA
Temperate Japonica	767	96.10%	3.70%	0.13%	0.13%	NA
Tropical Japonica	504	74.60%	0.80%	8.93%	15.67%	NA
Japonica Intermediate	241	86.70%	8.30%	1.24%	3.73%	NA
VI/Aromatic	96	21.90%	78.10%	0.00%	0.00%	NA
Intermediate	90	86.70%	5.60%	6.67%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0725407361	C -> DEL	N	N	silent_mutation	Average:85.684; most accessible tissue: Minghui63 flower, score: 96.754	N	N	N	N
vg0725407361	C -> T	LOC_Os07g42440.1	upstream_gene_variant ; 971.0bp to feature; MODIFIER	silent_mutation	Average:85.684; most accessible tissue: Minghui63 flower, score: 96.754	N	N	N	N
vg0725407361	C -> T	LOC_Os07g42440.4	upstream_gene_variant ; 971.0bp to feature; MODIFIER	silent_mutation	Average:85.684; most accessible tissue: Minghui63 flower, score: 96.754	N	N	N	N
vg0725407361	C -> T	LOC_Os07g42440.3	upstream_gene_variant ; 985.0bp to feature; MODIFIER	silent_mutation	Average:85.684; most accessible tissue: Minghui63 flower, score: 96.754	N	N	N	N
vg0725407361	C -> T	LOC_Os07g42440.2	upstream_gene_variant ; 985.0bp to feature; MODIFIER	silent_mutation	Average:85.684; most accessible tissue: Minghui63 flower, score: 96.754	N	N	N	N
vg0725407361	C -> T	LOC_Os07g42430.1	downstream_gene_variant ; 1409.0bp to feature; MODIFIER	silent_mutation	Average:85.684; most accessible tissue: Minghui63 flower, score: 96.754	N	N	N	N
vg0725407361	C -> T	LOC_Os07g42430-LOC_Os07g42440	intergenic_region ; MODIFIER	silent_mutation	Average:85.684; most accessible tissue: Minghui63 flower, score: 96.754	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)
vg0725407361	C	T	-0.04	-0.07	-0.03	-0.05	-0.02	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0725407361	NA	3.14E-08	mr1913	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
vg0725407361	4.92E-06	NA	mr1174_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
vg0725407361	NA	6.81E-06	mr1354_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
vg0725407361	NA	4.71E-07	mr1465_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
vg0725407361	1.30E-06	NA	mr1672_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
vg0725407361	2.89E-07	NA	mr1757_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
vg0725407361	NA	3.63E-06	mr1757_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
vg0725407361	NA	1.18E-06	mr1913_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