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Detailed information for vg0432961214:

Variant ID: vg0432961214 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32961214
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 191. )

Flanking Sequence (100 bp) in Reference Genome:

AAACTTTGGATCCAAACTTTCAATTTTTTCCATCACATCAACATGTCATACACATACAATTTTTCAGTCACATTGTACCAATTTCAACCCAAACTTTTAA[T/C]
TTTAGAAGGAACTAAACACAGCCTTAGTTTTAAACTTCCAACTTTTCCATCACATCAAAACTTTCCTACACACACATAAACTTCCAACTTTTCCGTCACA

Reverse complement sequence

TGTGACGGAAAAGTTGGAAGTTTATGTGTGTGTAGGAAAGTTTTGATGTGATGGAAAAGTTGGAAGTTTAAAACTAAGGCTGTGTTTAGTTCCTTCTAAA[A/G]
TTAAAAGTTTGGGTTGAAATTGGTACAATGTGACTGAAAAATTGTATGTGTATGACATGTTGATGTGATGGAAAAAATTGAAAGTTTGGATCCAAAGTTT

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	70.70%	29.10%	0.02%	0.19%	NA
All Indica	2759	97.40%	2.30%	0.04%	0.22%	NA
All Japonica	1512	24.70%	75.10%	0.00%	0.13%	NA
Aus	269	57.60%	42.40%	0.00%	0.00%	NA
Indica I	595	93.80%	5.70%	0.17%	0.34%	NA
Indica II	465	98.10%	1.50%	0.00%	0.43%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.70%	0.00%	0.25%	NA
Temperate Japonica	767	10.80%	89.20%	0.00%	0.00%	NA
Tropical Japonica	504	39.30%	60.50%	0.00%	0.20%	NA
Japonica Intermediate	241	38.60%	61.00%	0.00%	0.41%	NA
VI/Aromatic	96	62.50%	36.50%	0.00%	1.04%	NA
Intermediate	90	68.90%	31.10%	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
vg0432961214	T -> C	LOC_Os04g55410.1	upstream_gene_variant ; 1270.0bp to feature; MODIFIER	silent_mutation	Average:89.671; most accessible tissue: Zhenshan97 root, score: 97.213	N	N	N	N
vg0432961214	T -> C	LOC_Os04g55420.1	upstream_gene_variant ; 2058.0bp to feature; MODIFIER	silent_mutation	Average:89.671; most accessible tissue: Zhenshan97 root, score: 97.213	N	N	N	N
vg0432961214	T -> C	LOC_Os04g55410-LOC_Os04g55420	intergenic_region ; MODIFIER	silent_mutation	Average:89.671; most accessible tissue: Zhenshan97 root, score: 97.213	N	N	N	N
vg0432961214	T -> DEL	N	N	silent_mutation	Average:89.671; most accessible tissue: Zhenshan97 root, score: 97.213	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)
vg0432961214	T	C	0.0	-0.01	-0.02	0.0	0.0	0.0

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432961214	NA	6.57E-08	mr1040	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
vg0432961214	NA	1.72E-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
vg0432961214	2.37E-06	2.29E-09	mr1072_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
vg0432961214	NA	3.99E-08	mr1075_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
vg0432961214	NA	6.16E-07	mr1077_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
vg0432961214	NA	2.59E-06	mr1124_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
vg0432961214	NA	4.50E-08	mr1137_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
vg0432961214	6.16E-07	8.99E-10	mr1295_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
vg0432961214	NA	3.04E-06	mr1441_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
vg0432961214	NA	1.87E-07	mr1617_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