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Detailed information for vg0432638617:

Variant ID: vg0432638617 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32638617
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCCACCAAACTCTCGATCGCCACCACCAATCGGCTGCAGGCTTCTGCATGCCGGTGATCTGGATTAGTGGATGGCCACATCTATTATATATTAAAAGTC[T/C]
ATTAAACTTTGTATAAACCCTTCTAAACCGTCACATAGGACCCTTAAAAACGCTCCTACGCCGCCATGTGACGATCTATTAAGTTATAGAAATTCTAAAA

Reverse complement sequence

TTTTAGAATTTCTATAACTTAATAGATCGTCACATGGCGGCGTAGGAGCGTTTTTAAGGGTCCTATGTGACGGTTTAGAAGGGTTTATACAAAGTTTAAT[A/G]
GACTTTTAATATATAATAGATGTGGCCATCCACTAATCCAGATCACCGGCATGCAGAAGCCTGCAGCCGATTGGTGGTGGCGATCGAGAGTTTGGTGGCA

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	69.80%	28.00%	1.93%	0.28%	NA
All Indica	2759	71.90%	26.90%	0.76%	0.43%	NA
All Japonica	1512	69.40%	26.40%	4.17%	0.07%	NA
Aus	269	44.20%	55.40%	0.37%	0.00%	NA
Indica I	595	83.50%	14.80%	1.51%	0.17%	NA
Indica II	465	58.90%	39.60%	0.86%	0.65%	NA
Indica III	913	68.80%	30.60%	0.22%	0.44%	NA
Indica Intermediate	786	74.30%	24.40%	0.76%	0.51%	NA
Temperate Japonica	767	54.60%	37.80%	7.56%	0.00%	NA
Tropical Japonica	504	80.40%	19.00%	0.40%	0.20%	NA
Japonica Intermediate	241	93.40%	5.40%	1.24%	0.00%	NA
VI/Aromatic	96	84.40%	13.50%	2.08%	0.00%	NA
Intermediate	90	73.30%	22.20%	4.44%	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
vg0432638617	T -> C	LOC_Os04g54870.1	upstream_gene_variant ; 814.0bp to feature; MODIFIER	silent_mutation	Average:85.996; most accessible tissue: Minghui63 root, score: 95.947	N	N	N	N
vg0432638617	T -> C	LOC_Os04g54880.1	upstream_gene_variant ; 4885.0bp to feature; MODIFIER	silent_mutation	Average:85.996; most accessible tissue: Minghui63 root, score: 95.947	N	N	N	N
vg0432638617	T -> C	LOC_Os04g54870.2	upstream_gene_variant ; 780.0bp to feature; MODIFIER	silent_mutation	Average:85.996; most accessible tissue: Minghui63 root, score: 95.947	N	N	N	N
vg0432638617	T -> C	LOC_Os04g54860.1	downstream_gene_variant ; 3796.0bp to feature; MODIFIER	silent_mutation	Average:85.996; most accessible tissue: Minghui63 root, score: 95.947	N	N	N	N
vg0432638617	T -> C	LOC_Os04g54870-LOC_Os04g54880	intergenic_region ; MODIFIER	silent_mutation	Average:85.996; most accessible tissue: Minghui63 root, score: 95.947	N	N	N	N
vg0432638617	T -> DEL	N	N	silent_mutation	Average:85.996; most accessible tissue: Minghui63 root, score: 95.947	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)
vg0432638617	T	C	0.0	0.0	-0.01	-0.02	0.01	0.02

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432638617	NA	1.37E-12	mr1010_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
vg0432638617	NA	1.15E-09	mr1011_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
vg0432638617	NA	2.61E-06	mr1011_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
vg0432638617	2.32E-06	NA	mr1013_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
vg0432638617	NA	3.98E-08	mr1013_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
vg0432638617	NA	4.26E-07	mr1164_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
vg0432638617	NA	1.06E-06	mr1229_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
vg0432638617	NA	2.05E-07	mr1627_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
vg0432638617	NA	5.28E-09	mr1880_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